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**honey** · 01-27-2011, 02:05 PM

Cuffdiff out put

I will be curious to understand have you solved the following issues:
1. Combined GTF has both TSS_id and P_ids
2. Cuffdiff out put gives a one gene per row

If so please share how you solved these issues.

Thanks

**sramirez** · 01-30-2011, 12:54 PM

great thread!

**Novice** · 02-04-2011, 11:02 AM

Saved

I'll go with eveyone else here and say brilliant post starting this thread and great thread with very useful tips!!
I am one of those biologists who recently got a load of RNA-seq data to handle with no experience from programming at all. Been scratching my head for three weeks now and tried Avadis and on the way to try CLCBio.
If I get the Nobel at any point, I will acknowledge internet, google, SeqAnswers, and Jon Keats

**honey** · 02-04-2011, 11:30 AM

Novice,
I have used the beta version of Avadis and will be willing to know how it work. However I have not found toll as user friendly as Gene Spring. The level of customer support has alos declined...

**Jon_Keats** · 02-13-2011, 09:40 PM

Joining the Circos

I've recently been working on finalizing one of my old post-doc papers and decided a Circos (http://mkweb.bcgsc.ca/circos/) plot would be a nice way to show the results of WGS, RNAseq, and copy number datasets. Unlike most applications there is a great tutorial on the website that will take you through all the steps but it is great/long and I suspect 90% of the people on this forum will be generating the same plots that doesn't seem to be covered as a single tutorial example. So here is my version:

Step 1 - Download the Circos distribution (http://mkweb.bcgsc.ca/circos/software/download/)

-Currently, download "circos-0.52.tgz" which is the main distribution
-Also, download "circos-0.52-4.tgz" which contains two updates
-Move both to /ngs/applications and unpack
*Replace the old "circos" binary in circos-0.52/bin with the one in the circos-0.52-4.tgz download
*Replace the old "circos.pm" file in circos-0.52/lib with the one is the circos-0.52-4.tgz download

Step 2 - Setup the Circos perl binary and update your perl distribution

1) Open up terminal
2) type "which perl"
- On a Mac it should return: /usr/bin/perl
3) Open up the updated "circos" binary in circos-0.52/bin
Should look like this

Code:

#!/bin/env perl

=pod

=head1 NAME

                                    ____ _
                                   / ___(_)_ __ ___ ___  ___
                                  | |   | | '__/ __/ _ \/ __|
                                  | |___| | | | (_| (_) \__ \
                                   \____|_|_|  \___\___/|___/

                                                round is good

circos - generate publication-quality, circularly-composited plots 
    of data and annotations layered on chromosome ideograms

4) Update the first line so it indicates the location of your perl distribution we just identified (ie. /usr/bin/perl)
Should now look like

Code:

#!/usr/bin/perl

=pod

=head1 NAME

5) Update your perl distribution so it has all the required packages that circos will use to make pretty pictures for you

- In terminal type "sudo perl -MCPAN -e shell"
NOTE: I found things didn't work correctly unless I used sudo
- Answer the prompts
- Install the following modules by typing "install module" (ie. install Clone or install GD::Polyline)
NOTE: I retyped the each install command after each install to confirm the install, plus you will likely see an error about YLIM? (sorry can't remember exactly) but you can disregard. Also for some reason the "Clone" install only worked for me after I install all the others so I've moved it to the bottom of the list. Last I needed to install one final package not directly suggested by the circos website (Config::General).

Modules to install: (You will need to manually install GD from here: http://www.boutell.com/gd/manual2.0.28.html#getgd.)
GD
GD::Polyline
List::Util
Math::Bezier
Math::BigFloat
Math::Round
Math::VecStat
Params::Validate (must update Module::Build before properly running, so install Module::Build)
Readonly
Set::IntSpan
Clone
Config::General
Graphics::ColorObject

Okay you are now ready to run the tutorials listed on the website. I'm going to update this post in the coming days will a setup file that most people could use but right now I have to finish this paper first.

***Update***

Step 3 - Test the circos install

1) In terminal navigate to the circos directory (ex. cd ngs/applications/circos-0.52)
2) Make a temporary directory by typing "mkdir temp"
3) Run the 2/2 tutorial as a test by typing "bin/circos -conf tutorials/2/2/circos.conf -outputdir temp -outputfile test1.png"
**This should only take a couple of seconds, maybe a minute on a slow system and generate a plot of each human chromosome in different colors**

***My Setup***

1) Copy the binary and library files to your path directory so you can just type "circos" instead of "bin/circos" each time
**In case you follow this thread as follows**

Code:

cd ngs/applications/circos-0.52/bin
cp circos $HOME/local/bin
cd ../lib
cp circos.pm $HOME/local/lib

2) In the circos-0.52 directory create a couple of directories for your usage

Code:

cd ngs/applications/circos-0.52
mkdir my_plots
mkdir my_reference_files
mkdir my_config_files
mkdir my_data_files

3) Populate your reference files. Most of what I'm listing are just modified versions of ones in the tutorials and I built the hg19 karyotype following the website suggestions.

hg18_karyotype_white.txt

Code:

# Human chromsome sizes and cytogenetic band position.
# Data based on hg18 assembly.
chr - hs1 1 0 247249719 white
chr - hs2 2 0 242951149 white
chr - hs3 3 0 199501827 white
chr - hs4 4 0 191273063 white
chr - hs5 5 0 180857866 white
chr - hs6 6 0 170899992 white
chr - hs7 7 0 158821424 white
chr - hs8 8 0 146274826 white
chr - hs9 9 0 140273252 white
chr - hs10 10 0 135374737 white
chr - hs11 11 0 134452384 white
chr - hs12 12 0 132349534 white
chr - hs13 13 0 114142980 white
chr - hs14 14 0 106368585 white
chr - hs15 15 0 100338915 white
chr - hs16 16 0 88827254 white
chr - hs17 17 0 78774742 white
chr - hs18 18 0 76117153 white
chr - hs19 19 0 63811651 white
chr - hs20 20 0 62435964 white
chr - hs21 21 0 46944323 white
chr - hs22 22 0 49691432 white
chr - hsX X 0 154913754 white
chr - hsY Y 0 57772954 white
band hs1 p36.33 p36.33 0 2300000 gneg
band hs1 p36.32 p36.32 2300000 5300000 gpos25
band hs1 p36.31 p36.31 5300000 7100000 gneg
band hs1 p36.23 p36.23 7100000 9200000 gpos25
band hs1 p36.22 p36.22 9200000 12600000 gneg
band hs1 p36.21 p36.21 12600000 16100000 gpos50
band hs1 p36.13 p36.13 16100000 20300000 gneg
band hs1 p36.12 p36.12 20300000 23800000 gpos25
band hs1 p36.11 p36.11 23800000 27800000 gneg
band hs1 p35.3 p35.3 27800000 30000000 gpos25
band hs1 p35.2 p35.2 30000000 32200000 gneg
band hs1 p35.1 p35.1 32200000 34400000 gpos25
band hs1 p34.3 p34.3 34400000 39600000 gneg
band hs1 p34.2 p34.2 39600000 43900000 gpos25
band hs1 p34.1 p34.1 43900000 46500000 gneg
band hs1 p33 p33 46500000 51300000 gpos75
band hs1 p32.3 p32.3 51300000 56200000 gneg
band hs1 p32.2 p32.2 56200000 58700000 gpos50
band hs1 p32.1 p32.1 58700000 60900000 gneg
band hs1 p31.3 p31.3 60900000 68700000 gpos50
band hs1 p31.2 p31.2 68700000 69500000 gneg
band hs1 p31.1 p31.1 69500000 84700000 gpos100
band hs1 p22.3 p22.3 84700000 88100000 gneg
band hs1 p22.2 p22.2 88100000 92000000 gpos75
band hs1 p22.1 p22.1 92000000 94500000 gneg
band hs1 p21.3 p21.3 94500000 99400000 gpos75
band hs1 p21.2 p21.2 99400000 102000000 gneg
band hs1 p21.1 p21.1 102000000 107000000 gpos100
band hs1 p13.3 p13.3 107000000 111600000 gneg
band hs1 p13.2 p13.2 111600000 115900000 gpos50
band hs1 p13.1 p13.1 115900000 117600000 gneg
band hs1 p12 p12 117600000 120700000 gpos50
band hs1 p11.2 p11.2 120700000 121100000 gneg
band hs1 p11.1 p11.1 121100000 124300000 acen
band hs1 q11 q11 124300000 128000000 acen
band hs1 q12 q12 128000000 142400000 gvar
band hs1 q21.1 q21.1 142400000 148000000 gneg
band hs1 q21.2 q21.2 148000000 149600000 gpos50
band hs1 q21.3 q21.3 149600000 153300000 gneg
band hs1 q22 q22 153300000 154800000 gpos50
band hs1 q23.1 q23.1 154800000 157300000 gneg
band hs1 q23.2 q23.2 157300000 158800000 gpos50
band hs1 q23.3 q23.3 158800000 163800000 gneg
band hs1 q24.1 q24.1 163800000 165500000 gpos50
band hs1 q24.2 q24.2 165500000 169100000 gneg
band hs1 q24.3 q24.3 169100000 171200000 gpos75
band hs1 q25.1 q25.1 171200000 174300000 gneg
band hs1 q25.2 q25.2 174300000 178600000 gpos50
band hs1 q25.3 q25.3 178600000 184000000 gneg
band hs1 q31.1 q31.1 184000000 189000000 gpos100
band hs1 q31.2 q31.2 189000000 192100000 gneg
band hs1 q31.3 q31.3 192100000 197500000 gpos100
band hs1 q32.1 q32.1 197500000 205300000 gneg
band hs1 q32.2 q32.2 205300000 209500000 gpos25
band hs1 q32.3 q32.3 209500000 212100000 gneg
band hs1 q41 q41 212100000 222100000 gpos100
band hs1 q42.11 q42.11 222100000 222700000 gneg
band hs1 q42.12 q42.12 222700000 225100000 gpos25
band hs1 q42.13 q42.13 225100000 228800000 gneg
band hs1 q42.2 q42.2 228800000 232700000 gpos50
band hs1 q42.3 q42.3 232700000 234600000 gneg
band hs1 q43 q43 234600000 241700000 gpos75
band hs1 q44 q44 241700000 247249719 gneg
band hs2 p25.3 p25.3 0 4300000 gneg
band hs2 p25.2 p25.2 4300000 7000000 gpos50
band hs2 p25.1 p25.1 7000000 12800000 gneg
band hs2 p24.3 p24.3 12800000 17000000 gpos75
band hs2 p24.2 p24.2 17000000 19100000 gneg
band hs2 p24.1 p24.1 19100000 23900000 gpos75
band hs2 p23.3 p23.3 23900000 27700000 gneg
band hs2 p23.2 p23.2 27700000 29800000 gpos25
band hs2 p23.1 p23.1 29800000 31900000 gneg
band hs2 p22.3 p22.3 31900000 36400000 gpos75
band hs2 p22.2 p22.2 36400000 38400000 gneg
band hs2 p22.1 p22.1 38400000 41600000 gpos50
band hs2 p21 p21 41600000 47600000 gneg
band hs2 p16.3 p16.3 47600000 52700000 gpos100
band hs2 p16.2 p16.2 52700000 54800000 gneg
band hs2 p16.1 p16.1 54800000 61100000 gpos100
band hs2 p15 p15 61100000 64000000 gneg
band hs2 p14 p14 64000000 70500000 gpos50
band hs2 p13.3 p13.3 70500000 72600000 gneg
band hs2 p13.2 p13.2 72600000 73900000 gpos50
band hs2 p13.1 p13.1 73900000 75400000 gneg
band hs2 p12 p12 75400000 83700000 gpos100
band hs2 p11.2 p11.2 83700000 91000000 gneg
band hs2 p11.1 p11.1 91000000 93300000 acen
band hs2 q11.1 q11.1 93300000 95700000 acen
band hs2 q11.2 q11.2 95700000 102100000 gneg
band hs2 q12.1 q12.1 102100000 105300000 gpos50
band hs2 q12.2 q12.2 105300000 106700000 gneg
band hs2 q12.3 q12.3 106700000 108600000 gpos25
band hs2 q13 q13 108600000 113800000 gneg
band hs2 q14.1 q14.1 113800000 118600000 gpos50
band hs2 q14.2 q14.2 118600000 122100000 gneg
band hs2 q14.3 q14.3 122100000 129600000 gpos50
band hs2 q21.1 q21.1 129600000 132200000 gneg
band hs2 q21.2 q21.2 132200000 134800000 gpos25
band hs2 q21.3 q21.3 134800000 136600000 gneg
band hs2 q22.1 q22.1 136600000 142400000 gpos100
band hs2 q22.2 q22.2 142400000 144700000 gneg
band hs2 q22.3 q22.3 144700000 148400000 gpos100
band hs2 q23.1 q23.1 148400000 149600000 gneg
band hs2 q23.2 q23.2 149600000 150300000 gpos25
band hs2 q23.3 q23.3 150300000 154600000 gneg
band hs2 q24.1 q24.1 154600000 159600000 gpos75
band hs2 q24.2 q24.2 159600000 163500000 gneg
band hs2 q24.3 q24.3 163500000 169500000 gpos75
band hs2 q31.1 q31.1 169500000 177700000 gneg
band hs2 q31.2 q31.2 177700000 180400000 gpos50
band hs2 q31.3 q31.3 180400000 182700000 gneg
band hs2 q32.1 q32.1 182700000 189100000 gpos75
band hs2 q32.2 q32.2 189100000 191600000 gneg
band hs2 q32.3 q32.3 191600000 197100000 gpos75
band hs2 q33.1 q33.1 197100000 203500000 gneg
band hs2 q33.2 q33.2 203500000 205600000 gpos50
band hs2 q33.3 q33.3 205600000 209100000 gneg
band hs2 q34 q34 209100000 215100000 gpos100
band hs2 q35 q35 215100000 221300000 gneg
band hs2 q36.1 q36.1 221300000 224900000 gpos75
band hs2 q36.2 q36.2 224900000 225800000 gneg
band hs2 q36.3 q36.3 225800000 230700000 gpos100
band hs2 q37.1 q37.1 230700000 235300000 gneg
band hs2 q37.2 q37.2 235300000 237000000 gpos50
band hs2 q37.3 q37.3 237000000 242951149 gneg
band hs3 p26.3 p26.3 0 3500000 gpos50
band hs3 p26.2 p26.2 3500000 5500000 gneg
band hs3 p26.1 p26.1 5500000 8700000 gpos50
band hs3 p25.3 p25.3 8700000 11500000 gneg
band hs3 p25.2 p25.2 11500000 12400000 gpos25
band hs3 p25.1 p25.1 12400000 14700000 gneg
band hs3 p24.3 p24.3 14700000 23800000 gpos100
band hs3 p24.2 p24.2 23800000 26400000 gneg
band hs3 p24.1 p24.1 26400000 30800000 gpos75
band hs3 p23 p23 30800000 32100000 gneg
band hs3 p22.3 p22.3 32100000 36500000 gpos50
band hs3 p22.2 p22.2 36500000 39300000 gneg
band hs3 p22.1 p22.1 39300000 43600000 gpos75
band hs3 p21.33 p21.33 43600000 44400000 gneg
band hs3 p21.32 p21.32 44400000 44700000 gpos50
band hs3 p21.31 p21.31 44700000 51400000 gneg
band hs3 p21.2 p21.2 51400000 51700000 gpos25
band hs3 p21.1 p21.1 51700000 54400000 gneg
band hs3 p14.3 p14.3 54400000 58500000 gpos50
band hs3 p14.2 p14.2 58500000 63700000 gneg
band hs3 p14.1 p14.1 63700000 71800000 gpos50
band hs3 p13 p13 71800000 74200000 gneg
band hs3 p12.3 p12.3 74200000 81800000 gpos75
band hs3 p12.2 p12.2 81800000 83700000 gneg
band hs3 p12.1 p12.1 83700000 87200000 gpos75
band hs3 p11.2 p11.2 87200000 89400000 gneg
band hs3 p11.1 p11.1 89400000 91700000 acen
band hs3 q11.1 q11.1 91700000 93200000 acen
band hs3 q11.2 q11.2 93200000 99800000 gvar
band hs3 q12.1 q12.1 99800000 101500000 gneg
band hs3 q12.2 q12.2 101500000 102500000 gpos25
band hs3 q12.3 q12.3 102500000 104400000 gneg
band hs3 q13.11 q13.11 104400000 107800000 gpos75
band hs3 q13.12 q13.12 107800000 109500000 gneg
band hs3 q13.13 q13.13 109500000 112800000 gpos50
band hs3 q13.2 q13.2 112800000 115000000 gneg
band hs3 q13.31 q13.31 115000000 118800000 gpos75
band hs3 q13.32 q13.32 118800000 120500000 gneg
band hs3 q13.33 q13.33 120500000 123400000 gpos75
band hs3 q21.1 q21.1 123400000 125400000 gneg
band hs3 q21.2 q21.2 125400000 127700000 gpos25
band hs3 q21.3 q21.3 127700000 131500000 gneg
band hs3 q22.1 q22.1 131500000 135700000 gpos25
band hs3 q22.2 q22.2 135700000 137400000 gneg
band hs3 q22.3 q22.3 137400000 140400000 gpos25
band hs3 q23 q23 140400000 144400000 gneg
band hs3 q24 q24 144400000 150400000 gpos100
band hs3 q25.1 q25.1 150400000 153500000 gneg
band hs3 q25.2 q25.2 153500000 156300000 gpos50
band hs3 q25.31 q25.31 156300000 158100000 gneg
band hs3 q25.32 q25.32 158100000 159900000 gpos50
band hs3 q25.33 q25.33 159900000 161200000 gneg
band hs3 q26.1 q26.1 161200000 169200000 gpos100
band hs3 q26.2 q26.2 169200000 172500000 gneg
band hs3 q26.31 q26.31 172500000 177300000 gpos75
band hs3 q26.32 q26.32 177300000 180600000 gneg
band hs3 q26.33 q26.33 180600000 184200000 gpos75
band hs3 q27.1 q27.1 184200000 186000000 gneg
band hs3 q27.2 q27.2 186000000 187500000 gpos25
band hs3 q27.3 q27.3 187500000 189400000 gneg
band hs3 q28 q28 189400000 193800000 gpos75
band hs3 q29 q29 193800000 199501827 gneg
band hs4 p16.3 p16.3 0 3100000 gneg
band hs4 p16.2 p16.2 3100000 5200000 gpos25
band hs4 p16.1 p16.1 5200000 10900000 gneg
band hs4 p15.33 p15.33 10900000 15300000 gpos50
band hs4 p15.32 p15.32 15300000 18500000 gneg
band hs4 p15.31 p15.31 18500000 23100000 gpos75
band hs4 p15.2 p15.2 23100000 27900000 gneg
band hs4 p15.1 p15.1 27900000 35500000 gpos100
band hs4 p14 p14 35500000 40900000 gneg
band hs4 p13 p13 40900000 45600000 gpos50
band hs4 p12 p12 45600000 48700000 gneg
band hs4 p11 p11 48700000 50700000 acen
band hs4 q11 q11 50700000 52400000 acen
band hs4 q12 q12 52400000 59200000 gneg
band hs4 q13.1 q13.1 59200000 66300000 gpos100
band hs4 q13.2 q13.2 66300000 70400000 gneg
band hs4 q13.3 q13.3 70400000 76500000 gpos75
band hs4 q21.1 q21.1 76500000 79200000 gneg
band hs4 q21.21 q21.21 79200000 82600000 gpos50
band hs4 q21.22 q21.22 82600000 84300000 gneg
band hs4 q21.23 q21.23 84300000 87100000 gpos25
band hs4 q21.3 q21.3 87100000 88200000 gneg
band hs4 q22.1 q22.1 88200000 94000000 gpos75
band hs4 q22.2 q22.2 94000000 95400000 gneg
band hs4 q22.3 q22.3 95400000 99100000 gpos75
band hs4 q23 q23 99100000 102500000 gneg
band hs4 q24 q24 102500000 107900000 gpos50
band hs4 q25 q25 107900000 114100000 gneg
band hs4 q26 q26 114100000 120600000 gpos75
band hs4 q27 q27 120600000 124000000 gneg
band hs4 q28.1 q28.1 124000000 129100000 gpos50
band hs4 q28.2 q28.2 129100000 131300000 gneg
band hs4 q28.3 q28.3 131300000 139500000 gpos100
band hs4 q31.1 q31.1 139500000 141700000 gneg
band hs4 q31.21 q31.21 141700000 145000000 gpos25
band hs4 q31.22 q31.22 145000000 147700000 gneg
band hs4 q31.23 q31.23 147700000 151000000 gpos25
band hs4 q31.3 q31.3 151000000 155100000 gneg
band hs4 q32.1 q32.1 155100000 161500000 gpos100
band hs4 q32.2 q32.2 161500000 164500000 gneg
band hs4 q32.3 q32.3 164500000 170400000 gpos100
band hs4 q33 q33 170400000 172200000 gneg
band hs4 q34.1 q34.1 172200000 176600000 gpos75
band hs4 q34.2 q34.2 176600000 177800000 gneg
band hs4 q34.3 q34.3 177800000 182600000 gpos100
band hs4 q35.1 q35.1 182600000 187300000 gneg
band hs4 q35.2 q35.2 187300000 191273063 gpos25
band hs5 p15.33 p15.33 0 4400000 gneg
band hs5 p15.32 p15.32 4400000 6000000 gpos25
band hs5 p15.31 p15.31 6000000 8200000 gneg
band hs5 p15.2 p15.2 8200000 15100000 gpos50
band hs5 p15.1 p15.1 15100000 18500000 gneg
band hs5 p14.3 p14.3 18500000 23300000 gpos100
band hs5 p14.2 p14.2 23300000 24700000 gneg
band hs5 p14.1 p14.1 24700000 29300000 gpos100
band hs5 p13.3 p13.3 29300000 34400000 gneg
band hs5 p13.2 p13.2 34400000 38500000 gpos25
band hs5 p13.1 p13.1 38500000 42400000 gneg
band hs5 p12 p12 42400000 45800000 gpos50
band hs5 p11 p11 45800000 47700000 acen
band hs5 q11.1 q11.1 47700000 50500000 acen
band hs5 q11.2 q11.2 50500000 58900000 gneg
band hs5 q12.1 q12.1 58900000 63000000 gpos75
band hs5 q12.2 q12.2 63000000 63700000 gneg
band hs5 q12.3 q12.3 63700000 66500000 gpos75
band hs5 q13.1 q13.1 66500000 68400000 gneg
band hs5 q13.2 q13.2 68400000 73300000 gpos50
band hs5 q13.3 q13.3 73300000 76400000 gneg
band hs5 q14.1 q14.1 76400000 81300000 gpos50
band hs5 q14.2 q14.2 81300000 82800000 gneg
band hs5 q14.3 q14.3 82800000 91900000 gpos100
band hs5 q15 q15 91900000 97300000 gneg
band hs5 q21.1 q21.1 97300000 102800000 gpos100
band hs5 q21.2 q21.2 102800000 104500000 gneg
band hs5 q21.3 q21.3 104500000 109600000 gpos100
band hs5 q22.1 q22.1 109600000 111500000 gneg
band hs5 q22.2 q22.2 111500000 113100000 gpos50
band hs5 q22.3 q22.3 113100000 115200000 gneg
band hs5 q23.1 q23.1 115200000 121500000 gpos100
band hs5 q23.2 q23.2 121500000 127300000 gneg
band hs5 q23.3 q23.3 127300000 130400000 gpos100
band hs5 q31.1 q31.1 130400000 135400000 gneg
band hs5 q31.2 q31.2 135400000 139000000 gpos25
band hs5 q31.3 q31.3 139000000 143100000 gneg
band hs5 q32 q32 143100000 147200000 gpos75
band hs5 q33.1 q33.1 147200000 152100000 gneg
band hs5 q33.2 q33.2 152100000 155600000 gpos50
band hs5 q33.3 q33.3 155600000 159900000 gneg
band hs5 q34 q34 159900000 167400000 gpos100
band hs5 q35.1 q35.1 167400000 172200000 gneg
band hs5 q35.2 q35.2 172200000 176500000 gpos25
band hs5 q35.3 q35.3 176500000 180857866 gneg
band hs6 p25.3 p25.3 0 2300000 gneg
band hs6 p25.2 p25.2 2300000 4100000 gpos25
band hs6 p25.1 p25.1 4100000 7000000 gneg
band hs6 p24.3 p24.3 7000000 10600000 gpos50
band hs6 p24.2 p24.2 10600000 11200000 gneg
band hs6 p24.1 p24.1 11200000 13500000 gpos25
band hs6 p23 p23 13500000 15500000 gneg
band hs6 p22.3 p22.3 15500000 23500000 gpos75
band hs6 p22.2 p22.2 23500000 26100000 gneg
band hs6 p22.1 p22.1 26100000 29900000 gpos50
band hs6 p21.33 p21.33 29900000 31900000 gneg
band hs6 p21.32 p21.32 31900000 33600000 gpos25
band hs6 p21.31 p21.31 33600000 36800000 gneg
band hs6 p21.2 p21.2 36800000 40600000 gpos25
band hs6 p21.1 p21.1 40600000 45200000 gneg
band hs6 p12.3 p12.3 45200000 51100000 gpos100
band hs6 p12.2 p12.2 51100000 52600000 gneg
band hs6 p12.1 p12.1 52600000 57200000 gpos100
band hs6 p11.2 p11.2 57200000 58400000 gneg
band hs6 p11.1 p11.1 58400000 60500000 acen
band hs6 q11.1 q11.1 60500000 63400000 acen
band hs6 q11.2 q11.2 63400000 63500000 gneg
band hs6 q12 q12 63500000 70000000 gpos100
band hs6 q13 q13 70000000 75900000 gneg
band hs6 q14.1 q14.1 75900000 83900000 gpos50
band hs6 q14.2 q14.2 83900000 84700000 gneg
band hs6 q14.3 q14.3 84700000 87500000 gpos50
band hs6 q15 q15 87500000 92100000 gneg
band hs6 q16.1 q16.1 92100000 98700000 gpos100
band hs6 q16.2 q16.2 98700000 99900000 gneg
band hs6 q16.3 q16.3 99900000 104800000 gpos100
band hs6 q21 q21 104800000 113900000 gneg
band hs6 q22.1 q22.1 113900000 117100000 gpos75
band hs6 q22.2 q22.2 117100000 118600000 gneg
band hs6 q22.31 q22.31 118600000 126200000 gpos100
band hs6 q22.32 q22.32 126200000 127300000 gneg
band hs6 q22.33 q22.33 127300000 130400000 gpos75
band hs6 q23.1 q23.1 130400000 131300000 gneg
band hs6 q23.2 q23.2 131300000 135200000 gpos50
band hs6 q23.3 q23.3 135200000 139100000 gneg
band hs6 q24.1 q24.1 139100000 142900000 gpos75
band hs6 q24.2 q24.2 142900000 145700000 gneg
band hs6 q24.3 q24.3 145700000 149100000 gpos75
band hs6 q25.1 q25.1 149100000 152600000 gneg
band hs6 q25.2 q25.2 152600000 155600000 gpos50
band hs6 q25.3 q25.3 155600000 160900000 gneg
band hs6 q26 q26 160900000 164400000 gpos50
band hs6 q27 q27 164400000 170899992 gneg
band hs7 p22.3 p22.3 0 2100000 gneg
band hs7 p22.2 p22.2 2100000 4500000 gpos25
band hs7 p22.1 p22.1 4500000 7200000 gneg
band hs7 p21.3 p21.3 7200000 13300000 gpos100
band hs7 p21.2 p21.2 13300000 15200000 gneg
band hs7 p21.1 p21.1 15200000 19500000 gpos100
band hs7 p15.3 p15.3 19500000 24900000 gneg
band hs7 p15.2 p15.2 24900000 28000000 gpos50
band hs7 p15.1 p15.1 28000000 31800000 gneg
band hs7 p14.3 p14.3 31800000 35600000 gpos75
band hs7 p14.2 p14.2 35600000 37500000 gneg
band hs7 p14.1 p14.1 37500000 43300000 gpos75
band hs7 p13 p13 43300000 46600000 gneg
band hs7 p12.3 p12.3 46600000 49800000 gpos75
band hs7 p12.2 p12.2 49800000 50900000 gneg
band hs7 p12.1 p12.1 50900000 53900000 gpos75
band hs7 p11.2 p11.2 53900000 57400000 gneg
band hs7 p11.1 p11.1 57400000 59100000 acen
band hs7 q11.1 q11.1 59100000 61100000 acen
band hs7 q11.21 q11.21 61100000 66100000 gneg
band hs7 q11.22 q11.22 66100000 71800000 gpos50
band hs7 q11.23 q11.23 71800000 77400000 gneg
band hs7 q21.11 q21.11 77400000 86200000 gpos100
band hs7 q21.12 q21.12 86200000 88000000 gneg
band hs7 q21.13 q21.13 88000000 90900000 gpos75
band hs7 q21.2 q21.2 90900000 92600000 gneg
band hs7 q21.3 q21.3 92600000 97900000 gpos75
band hs7 q22.1 q22.1 97900000 104400000 gneg
band hs7 q22.2 q22.2 104400000 105900000 gpos50
band hs7 q22.3 q22.3 105900000 107200000 gneg
band hs7 q31.1 q31.1 107200000 114400000 gpos75
band hs7 q31.2 q31.2 114400000 117200000 gneg
band hs7 q31.31 q31.31 117200000 120900000 gpos75
band hs7 q31.32 q31.32 120900000 123600000 gneg
band hs7 q31.33 q31.33 123600000 126900000 gpos75
band hs7 q32.1 q32.1 126900000 129000000 gneg
band hs7 q32.2 q32.2 129000000 130100000 gpos25
band hs7 q32.3 q32.3 130100000 132400000 gneg
band hs7 q33 q33 132400000 137300000 gpos50
band hs7 q34 q34 137300000 142800000 gneg
band hs7 q35 q35 142800000 147500000 gpos75
band hs7 q36.1 q36.1 147500000 152200000 gneg
band hs7 q36.2 q36.2 152200000 154700000 gpos25
band hs7 q36.3 q36.3 154700000 158821424 gneg
band hs8 p23.3 p23.3 0 2200000 gneg
band hs8 p23.2 p23.2 2200000 6200000 gpos75
band hs8 p23.1 p23.1 6200000 12700000 gneg
band hs8 p22 p22 12700000 19100000 gpos100
band hs8 p21.3 p21.3 19100000 23400000 gneg
band hs8 p21.2 p21.2 23400000 27400000 gpos50
band hs8 p21.1 p21.1 27400000 29700000 gneg
band hs8 p12 p12 29700000 38500000 gpos75
band hs8 p11.23 p11.23 38500000 39500000 gneg
band hs8 p11.22 p11.22 39500000 39900000 gpos25
band hs8 p11.21 p11.21 39900000 43200000 gneg
band hs8 p11.1 p11.1 43200000 45200000 acen
band hs8 q11.1 q11.1 45200000 48100000 acen
band hs8 q11.21 q11.21 48100000 50400000 gneg
band hs8 q11.22 q11.22 50400000 52800000 gpos75
band hs8 q11.23 q11.23 52800000 55600000 gneg
band hs8 q12.1 q12.1 55600000 61700000 gpos50
band hs8 q12.2 q12.2 61700000 62400000 gneg
band hs8 q12.3 q12.3 62400000 66100000 gpos50
band hs8 q13.1 q13.1 66100000 68100000 gneg
band hs8 q13.2 q13.2 68100000 70600000 gpos50
band hs8 q13.3 q13.3 70600000 74000000 gneg
band hs8 q21.11 q21.11 74000000 78500000 gpos100
band hs8 q21.12 q21.12 78500000 80300000 gneg
band hs8 q21.13 q21.13 80300000 84900000 gpos75
band hs8 q21.2 q21.2 84900000 87200000 gneg
band hs8 q21.3 q21.3 87200000 93500000 gpos100
band hs8 q22.1 q22.1 93500000 99100000 gneg
band hs8 q22.2 q22.2 99100000 101600000 gpos25
band hs8 q22.3 q22.3 101600000 106100000 gneg
band hs8 q23.1 q23.1 106100000 110600000 gpos75
band hs8 q23.2 q23.2 110600000 112200000 gneg
band hs8 q23.3 q23.3 112200000 117700000 gpos100
band hs8 q24.11 q24.11 117700000 119200000 gneg
band hs8 q24.12 q24.12 119200000 122500000 gpos50
band hs8 q24.13 q24.13 122500000 127300000 gneg
band hs8 q24.21 q24.21 127300000 131500000 gpos50
band hs8 q24.22 q24.22 131500000 136500000 gneg
band hs8 q24.23 q24.23 136500000 140000000 gpos75
band hs8 q24.3 q24.3 140000000 146274826 gneg
band hs9 p24.3 p24.3 0 2200000 gneg
band hs9 p24.2 p24.2 2200000 4600000 gpos25
band hs9 p24.1 p24.1 4600000 9000000 gneg
band hs9 p23 p23 9000000 14100000 gpos75
band hs9 p22.3 p22.3 14100000 16600000 gneg
band hs9 p22.2 p22.2 16600000 18500000 gpos25
band hs9 p22.1 p22.1 18500000 19900000 gneg
band hs9 p21.3 p21.3 19900000 25500000 gpos100
band hs9 p21.2 p21.2 25500000 28100000 gneg
band hs9 p21.1 p21.1 28100000 32800000 gpos100
band hs9 p13.3 p13.3 32800000 36300000 gneg
band hs9 p13.2 p13.2 36300000 38000000 gpos25
band hs9 p13.1 p13.1 38000000 40200000 gneg
band hs9 p12 p12 40200000 42400000 gpos50
band hs9 p11.2 p11.2 42400000 46700000 gneg
band hs9 p11.1 p11.1 46700000 51800000 acen
band hs9 q11 q11 51800000 60300000 acen
band hs9 q12 q12 60300000 70000000 gvar
band hs9 q13 q13 70000000 70500000 gneg
band hs9 q21.11 q21.11 70500000 72700000 gpos25
band hs9 q21.12 q21.12 72700000 73100000 gneg
band hs9 q21.13 q21.13 73100000 79300000 gpos50
band hs9 q21.2 q21.2 79300000 80300000 gneg
band hs9 q21.31 q21.31 80300000 83400000 gpos50
band hs9 q21.32 q21.32 83400000 86100000 gneg
band hs9 q21.33 q21.33 86100000 89600000 gpos50
band hs9 q22.1 q22.1 89600000 91000000 gneg
band hs9 q22.2 q22.2 91000000 93000000 gpos25
band hs9 q22.31 q22.31 93000000 95600000 gneg
band hs9 q22.32 q22.32 95600000 98200000 gpos25
band hs9 q22.33 q22.33 98200000 101600000 gneg
band hs9 q31.1 q31.1 101600000 107200000 gpos100
band hs9 q31.2 q31.2 107200000 110300000 gneg
band hs9 q31.3 q31.3 110300000 113900000 gpos25
band hs9 q32 q32 113900000 116700000 gneg
band hs9 q33.1 q33.1 116700000 122000000 gpos75
band hs9 q33.2 q33.2 122000000 125800000 gneg
band hs9 q33.3 q33.3 125800000 129300000 gpos25
band hs9 q34.11 q34.11 129300000 132500000 gneg
band hs9 q34.12 q34.12 132500000 132800000 gpos25
band hs9 q34.13 q34.13 132800000 134900000 gneg
band hs9 q34.2 q34.2 134900000 136600000 gpos25
band hs9 q34.3 q34.3 136600000 140273252 gneg
band hsX p22.33 p22.33 0 4300000 gneg
band hsX p22.32 p22.32 4300000 6000000 gpos50
band hsX p22.31 p22.31 6000000 9500000 gneg
band hsX p22.2 p22.2 9500000 17100000 gpos50
band hsX p22.13 p22.13 17100000 19200000 gneg
band hsX p22.12 p22.12 19200000 21800000 gpos50
band hsX p22.11 p22.11 21800000 24900000 gneg
band hsX p21.3 p21.3 24900000 29400000 gpos100
band hsX p21.2 p21.2 29400000 31500000 gneg
band hsX p21.1 p21.1 31500000 37500000 gpos100
band hsX p11.4 p11.4 37500000 42300000 gneg
band hsX p11.3 p11.3 42300000 47300000 gpos75
band hsX p11.23 p11.23 47300000 49700000 gneg
band hsX p11.22 p11.22 49700000 54700000 gpos25
band hsX p11.21 p11.21 54700000 56600000 gneg
band hsX p11.1 p11.1 56600000 59500000 acen
band hsX q11.1 q11.1 59500000 65000000 acen
band hsX q11.2 q11.2 65000000 65100000 gneg
band hsX q12 q12 65100000 67700000 gpos50
band hsX q13.1 q13.1 67700000 72200000 gneg
band hsX q13.2 q13.2 72200000 73800000 gpos50
band hsX q13.3 q13.3 73800000 76000000 gneg
band hsX q21.1 q21.1 76000000 84500000 gpos100
band hsX q21.2 q21.2 84500000 86200000 gneg
band hsX q21.31 q21.31 86200000 91900000 gpos100
band hsX q21.32 q21.32 91900000 93500000 gneg
band hsX q21.33 q21.33 93500000 98200000 gpos75
band hsX q22.1 q22.1 98200000 102500000 gneg
band hsX q22.2 q22.2 102500000 103600000 gpos50
band hsX q22.3 q22.3 103600000 110500000 gneg
band hsX q23 q23 110500000 116800000 gpos75
band hsX q24 q24 116800000 120700000 gneg
band hsX q25 q25 120700000 129800000 gpos100
band hsX q26.1 q26.1 129800000 130300000 gneg
band hsX q26.2 q26.2 130300000 133500000 gpos25
band hsX q26.3 q26.3 133500000 137800000 gneg
band hsX q27.1 q27.1 137800000 140100000 gpos75
band hsX q27.2 q27.2 140100000 141900000 gneg
band hsX q27.3 q27.3 141900000 146900000 gpos100
band hsX q28 q28 146900000 154913754 gneg
band hsY p11.32 p11.32 0 1700000 gneg
band hsY p11.31 p11.31 1700000 3300000 gpos50
band hsY p11.2 p11.2 3300000 11200000 gneg
band hsY p11.1 p11.1 11200000 11300000 acen
band hsY q11.1 q11.1 11300000 12500000 acen
band hsY q11.21 q11.21 12500000 14300000 gneg
band hsY q11.221 q11.221 14300000 19000000 gpos50
band hsY q11.222 q11.222 19000000 21300000 gneg
band hsY q11.223 q11.223 21300000 25400000 gpos50
band hsY q11.23 q11.23 25400000 27200000 gneg
band hsY q12 q12 27200000 57772954 gvar
band hs10 p15.3 p15.3 0 3000000 gneg
band hs10 p15.2 p15.2 3000000 3800000 gpos25
band hs10 p15.1 p15.1 3800000 6700000 gneg
band hs10 p14 p14 6700000 12300000 gpos75
band hs10 p13 p13 12300000 17300000 gneg
band hs10 p12.33 p12.33 17300000 19900000 gpos75
band hs10 p12.32 p12.32 19900000 20500000 gneg
band hs10 p12.31 p12.31 20500000 22800000 gpos75
band hs10 p12.2 p12.2 22800000 24100000 gneg
band hs10 p12.1 p12.1 24100000 28300000 gpos50
band hs10 p11.23 p11.23 28300000 31400000 gneg
band hs10 p11.22 p11.22 31400000 34500000 gpos25
band hs10 p11.21 p11.21 34500000 38800000 gneg
band hs10 p11.1 p11.1 38800000 40300000 acen
band hs10 q11.1 q11.1 40300000 42100000 acen
band hs10 q11.21 q11.21 42100000 46100000 gneg
band hs10 q11.22 q11.22 46100000 50100000 gpos25
band hs10 q11.23 q11.23 50100000 53300000 gneg
band hs10 q21.1 q21.1 53300000 61200000 gpos100
band hs10 q21.2 q21.2 61200000 64800000 gneg
band hs10 q21.3 q21.3 64800000 71300000 gpos100
band hs10 q22.1 q22.1 71300000 74600000 gneg
band hs10 q22.2 q22.2 74600000 77400000 gpos50
band hs10 q22.3 q22.3 77400000 82000000 gneg
band hs10 q23.1 q23.1 82000000 87900000 gpos100
band hs10 q23.2 q23.2 87900000 89600000 gneg
band hs10 q23.31 q23.31 89600000 92900000 gpos75
band hs10 q23.32 q23.32 92900000 94200000 gneg
band hs10 q23.33 q23.33 94200000 98000000 gpos50
band hs10 q24.1 q24.1 98000000 99400000 gneg
band hs10 q24.2 q24.2 99400000 102000000 gpos50
band hs10 q24.31 q24.31 102000000 103000000 gneg
band hs10 q24.32 q24.32 103000000 104900000 gpos25
band hs10 q24.33 q24.33 104900000 105700000 gneg
band hs10 q25.1 q25.1 105700000 111800000 gpos100
band hs10 q25.2 q25.2 111800000 114900000 gneg
band hs10 q25.3 q25.3 114900000 119100000 gpos75
band hs10 q26.11 q26.11 119100000 121700000 gneg
band hs10 q26.12 q26.12 121700000 123100000 gpos50
band hs10 q26.13 q26.13 123100000 127400000 gneg
band hs10 q26.2 q26.2 127400000 130500000 gpos50
band hs10 q26.3 q26.3 130500000 135374737 gneg
band hs11 p15.5 p15.5 0 2800000 gneg
band hs11 p15.4 p15.4 2800000 10700000 gpos50
band hs11 p15.3 p15.3 10700000 12600000 gneg
band hs11 p15.2 p15.2 12600000 16100000 gpos50
band hs11 p15.1 p15.1 16100000 21600000 gneg
band hs11 p14.3 p14.3 21600000 26000000 gpos100
band hs11 p14.2 p14.2 26000000 27200000 gneg
band hs11 p14.1 p14.1 27200000 31000000 gpos75
band hs11 p13 p13 31000000 36400000 gneg
band hs11 p12 p12 36400000 43400000 gpos100
band hs11 p11.2 p11.2 43400000 48800000 gneg
band hs11 p11.12 p11.12 48800000 51400000 gpos75
band hs11 p11.11 p11.11 51400000 52900000 acen
band hs11 q11 q11 52900000 56400000 acen
band hs11 q12.1 q12.1 56400000 59700000 gpos75
band hs11 q12.2 q12.2 59700000 61400000 gneg
band hs11 q12.3 q12.3 61400000 63100000 gpos25
band hs11 q13.1 q13.1 63100000 67100000 gneg
band hs11 q13.2 q13.2 67100000 69200000 gpos25
band hs11 q13.3 q13.3 69200000 70700000 gneg
band hs11 q13.4 q13.4 70700000 74900000 gpos50
band hs11 q13.5 q13.5 74900000 76700000 gneg
band hs11 q14.1 q14.1 76700000 85300000 gpos100
band hs11 q14.2 q14.2 85300000 87900000 gneg
band hs11 q14.3 q14.3 87900000 92300000 gpos100
band hs11 q21 q21 92300000 96700000 gneg
band hs11 q22.1 q22.1 96700000 101600000 gpos100
band hs11 q22.2 q22.2 101600000 102400000 gneg
band hs11 q22.3 q22.3 102400000 110000000 gpos100
band hs11 q23.1 q23.1 110000000 112800000 gneg
band hs11 q23.2 q23.2 112800000 115400000 gpos50
band hs11 q23.3 q23.3 115400000 120700000 gneg
band hs11 q24.1 q24.1 120700000 123500000 gpos50
band hs11 q24.2 q24.2 123500000 127400000 gneg
band hs11 q24.3 q24.3 127400000 130300000 gpos50
band hs11 q25 q25 130300000 134452384 gneg
band hs12 p13.33 p13.33 0 3100000 gneg
band hs12 p13.32 p13.32 3100000 5300000 gpos25
band hs12 p13.31 p13.31 5300000 10000000 gneg
band hs12 p13.2 p13.2 10000000 12600000 gpos75
band hs12 p13.1 p13.1 12600000 14800000 gneg
band hs12 p12.3 p12.3 14800000 19900000 gpos100
band hs12 p12.2 p12.2 19900000 21200000 gneg
band hs12 p12.1 p12.1 21200000 26300000 gpos100
band hs12 p11.23 p11.23 26300000 27700000 gneg
band hs12 p11.22 p11.22 27700000 30600000 gpos50
band hs12 p11.21 p11.21 30600000 33200000 gneg
band hs12 p11.1 p11.1 33200000 35400000 acen
band hs12 q11 q11 35400000 36500000 acen
band hs12 q12 q12 36500000 44600000 gpos100
band hs12 q13.11 q13.11 44600000 47400000 gneg
band hs12 q13.12 q13.12 47400000 48400000 gpos25
band hs12 q13.13 q13.13 48400000 53100000 gneg
band hs12 q13.2 q13.2 53100000 55200000 gpos25
band hs12 q13.3 q13.3 55200000 56300000 gneg
band hs12 q14.1 q14.1 56300000 61400000 gpos75
band hs12 q14.2 q14.2 61400000 63400000 gneg
band hs12 q14.3 q14.3 63400000 66000000 gpos50
band hs12 q15 q15 66000000 69800000 gneg
band hs12 q21.1 q21.1 69800000 74100000 gpos75
band hs12 q21.2 q21.2 74100000 78700000 gneg
band hs12 q21.31 q21.31 78700000 85100000 gpos100
band hs12 q21.32 q21.32 85100000 87500000 gneg
band hs12 q21.33 q21.33 87500000 91200000 gpos100
band hs12 q22 q22 91200000 94800000 gneg
band hs12 q23.1 q23.1 94800000 100000000 gpos75
band hs12 q23.2 q23.2 100000000 102400000 gneg
band hs12 q23.3 q23.3 102400000 107500000 gpos50
band hs12 q24.11 q24.11 107500000 110200000 gneg
band hs12 q24.12 q24.12 110200000 110800000 gpos25
band hs12 q24.13 q24.13 110800000 112800000 gneg
band hs12 q24.21 q24.21 112800000 115300000 gpos50
band hs12 q24.22 q24.22 115300000 116700000 gneg
band hs12 q24.23 q24.23 116700000 119100000 gpos50
band hs12 q24.31 q24.31 119100000 124500000 gneg
band hs12 q24.32 q24.32 124500000 128700000 gpos50
band hs12 q24.33 q24.33 128700000 132349534 gneg
band hs13 p13 p13 0 3800000 gvar
band hs13 p12 p12 3800000 8300000 stalk
band hs13 p11.2 p11.2 8300000 13500000 gvar
band hs13 p11.1 p11.1 13500000 16000000 acen
band hs13 q11 q11 16000000 18400000 acen
band hs13 q12.11 q12.11 18400000 22200000 gneg
band hs13 q12.12 q12.12 22200000 24400000 gpos25
band hs13 q12.13 q12.13 24400000 26700000 gneg
band hs13 q12.2 q12.2 26700000 27800000 gpos25
band hs13 q12.3 q12.3 27800000 31100000 gneg
band hs13 q13.1 q13.1 31100000 32900000 gpos50
band hs13 q13.2 q13.2 32900000 34700000 gneg
band hs13 q13.3 q13.3 34700000 39500000 gpos75
band hs13 q14.11 q14.11 39500000 44300000 gneg
band hs13 q14.12 q14.12 44300000 45900000 gpos25
band hs13 q14.13 q14.13 45900000 46200000 gneg
band hs13 q14.2 q14.2 46200000 48900000 gpos50
band hs13 q14.3 q14.3 48900000 52200000 gneg
band hs13 q21.1 q21.1 52200000 57600000 gpos100
band hs13 q21.2 q21.2 57600000 60500000 gneg
band hs13 q21.31 q21.31 60500000 64100000 gpos75
band hs13 q21.32 q21.32 64100000 67200000 gneg
band hs13 q21.33 q21.33 67200000 72100000 gpos100
band hs13 q22.1 q22.1 72100000 74200000 gneg
band hs13 q22.2 q22.2 74200000 76000000 gpos50
band hs13 q22.3 q22.3 76000000 77800000 gneg
band hs13 q31.1 q31.1 77800000 86500000 gpos100
band hs13 q31.2 q31.2 86500000 88800000 gneg
band hs13 q31.3 q31.3 88800000 93800000 gpos100
band hs13 q32.1 q32.1 93800000 97000000 gneg
band hs13 q32.2 q32.2 97000000 98100000 gpos25
band hs13 q32.3 q32.3 98100000 100500000 gneg
band hs13 q33.1 q33.1 100500000 103700000 gpos100
band hs13 q33.2 q33.2 103700000 105800000 gneg
band hs13 q33.3 q33.3 105800000 109100000 gpos100
band hs13 q34 q34 109100000 114142980 gneg
band hs14 p13 p13 0 3100000 gvar
band hs14 p12 p12 3100000 6700000 stalk
band hs14 p11.2 p11.2 6700000 13600000 gvar
band hs14 p11.1 p11.1 13600000 15600000 acen
band hs14 q11.1 q11.1 15600000 19100000 acen
band hs14 q11.2 q11.2 19100000 23600000 gneg
band hs14 q12 q12 23600000 31800000 gpos100
band hs14 q13.1 q13.1 31800000 34100000 gneg
band hs14 q13.2 q13.2 34100000 35600000 gpos50
band hs14 q13.3 q13.3 35600000 36900000 gneg
band hs14 q21.1 q21.1 36900000 41000000 gpos100
band hs14 q21.2 q21.2 41000000 43200000 gneg
band hs14 q21.3 q21.3 43200000 48300000 gpos100
band hs14 q22.1 q22.1 48300000 52300000 gneg
band hs14 q22.2 q22.2 52300000 54400000 gpos25
band hs14 q22.3 q22.3 54400000 55800000 gneg
band hs14 q23.1 q23.1 55800000 61200000 gpos75
band hs14 q23.2 q23.2 61200000 64000000 gneg
band hs14 q23.3 q23.3 64000000 67000000 gpos50
band hs14 q24.1 q24.1 67000000 69300000 gneg
band hs14 q24.2 q24.2 69300000 72900000 gpos50
band hs14 q24.3 q24.3 72900000 78400000 gneg
band hs14 q31.1 q31.1 78400000 82600000 gpos100
band hs14 q31.2 q31.2 82600000 84000000 gneg
band hs14 q31.3 q31.3 84000000 88900000 gpos100
band hs14 q32.11 q32.11 88900000 90500000 gneg
band hs14 q32.12 q32.12 90500000 92800000 gpos25
band hs14 q32.13 q32.13 92800000 95400000 gneg
band hs14 q32.2 q32.2 95400000 100400000 gpos50
band hs14 q32.31 q32.31 100400000 102200000 gneg
band hs14 q32.32 q32.32 102200000 103000000 gpos50
band hs14 q32.33 q32.33 103000000 106368585 gneg
band hs15 p13 p13 0 3500000 gvar
band hs15 p12 p12 3500000 7900000 stalk
band hs15 p11.2 p11.2 7900000 14100000 gvar
band hs15 p11.1 p11.1 14100000 17000000 acen
band hs15 q11.1 q11.1 17000000 18400000 acen
band hs15 q11.2 q11.2 18400000 23300000 gneg
band hs15 q12 q12 23300000 25700000 gpos50
band hs15 q13.1 q13.1 25700000 28000000 gneg
band hs15 q13.2 q13.2 28000000 29000000 gpos50
band hs15 q13.3 q13.3 29000000 31400000 gneg
band hs15 q14 q14 31400000 37900000 gpos75
band hs15 q15.1 q15.1 37900000 40700000 gneg
band hs15 q15.2 q15.2 40700000 41400000 gpos25
band hs15 q15.3 q15.3 41400000 42700000 gneg
band hs15 q21.1 q21.1 42700000 47600000 gpos75
band hs15 q21.2 q21.2 47600000 51100000 gneg
band hs15 q21.3 q21.3 51100000 55800000 gpos75
band hs15 q22.1 q22.1 55800000 57100000 gneg
band hs15 q22.2 q22.2 57100000 61500000 gpos25
band hs15 q22.31 q22.31 61500000 64900000 gneg
band hs15 q22.32 q22.32 64900000 65000000 gpos25
band hs15 q22.33 q22.33 65000000 65300000 gneg
band hs15 q23 q23 65300000 70400000 gpos25
band hs15 q24.1 q24.1 70400000 73100000 gneg
band hs15 q24.2 q24.2 73100000 74400000 gpos25
band hs15 q24.3 q24.3 74400000 76100000 gneg
band hs15 q25.1 q25.1 76100000 79500000 gpos50
band hs15 q25.2 q25.2 79500000 83000000 gneg
band hs15 q25.3 q25.3 83000000 86900000 gpos50
band hs15 q26.1 q26.1 86900000 92100000 gneg
band hs15 q26.2 q26.2 92100000 96300000 gpos50
band hs15 q26.3 q26.3 96300000 100338915 gneg
band hs16 p13.3 p13.3 0 6300000 gneg
band hs16 p13.2 p13.2 6300000 10300000 gpos50
band hs16 p13.13 p13.13 10300000 12500000 gneg
band hs16 p13.12 p13.12 12500000 14700000 gpos50
band hs16 p13.11 p13.11 14700000 16700000 gneg
band hs16 p12.3 p12.3 16700000 20500000 gpos50
band hs16 p12.2 p12.2 20500000 21700000 gneg
band hs16 p12.1 p12.1 21700000 27600000 gpos50
band hs16 p11.2 p11.2 27600000 34400000 gneg
band hs16 p11.1 p11.1 34400000 38200000 acen
band hs16 q11.1 q11.1 38200000 40700000 acen
band hs16 q11.2 q11.2 40700000 45500000 gvar
band hs16 q12.1 q12.1 45500000 51200000 gneg
band hs16 q12.2 q12.2 51200000 54500000 gpos50
band hs16 q13 q13 54500000 56700000 gneg
band hs16 q21 q21 56700000 65200000 gpos100
band hs16 q22.1 q22.1 65200000 69400000 gneg
band hs16 q22.2 q22.2 69400000 69800000 gpos50
band hs16 q22.3 q22.3 69800000 73300000 gneg
band hs16 q23.1 q23.1 73300000 78200000 gpos75
band hs16 q23.2 q23.2 78200000 80500000 gneg
band hs16 q23.3 q23.3 80500000 82700000 gpos50
band hs16 q24.1 q24.1 82700000 85600000 gneg
band hs16 q24.2 q24.2 85600000 87200000 gpos25
band hs16 q24.3 q24.3 87200000 88827254 gneg
band hs17 p13.3 p13.3 0 3600000 gneg
band hs17 p13.2 p13.2 3600000 6800000 gpos50
band hs17 p13.1 p13.1 6800000 11200000 gneg
band hs17 p12 p12 11200000 15900000 gpos75
band hs17 p11.2 p11.2 15900000 22100000 gneg
band hs17 p11.1 p11.1 22100000 22200000 acen
band hs17 q11.1 q11.1 22200000 23200000 acen
band hs17 q11.2 q11.2 23200000 28800000 gneg
band hs17 q12 q12 28800000 35400000 gpos50
band hs17 q21.1 q21.1 35400000 35600000 gneg
band hs17 q21.2 q21.2 35600000 37800000 gpos25
band hs17 q21.31 q21.31 37800000 41900000 gneg
band hs17 q21.32 q21.32 41900000 44800000 gpos25
band hs17 q21.33 q21.33 44800000 47600000 gneg
band hs17 q22 q22 47600000 54900000 gpos75
band hs17 q23.1 q23.1 54900000 55600000 gneg
band hs17 q23.2 q23.2 55600000 58400000 gpos75
band hs17 q23.3 q23.3 58400000 59900000 gneg
band hs17 q24.1 q24.1 59900000 61600000 gpos50
band hs17 q24.2 q24.2 61600000 64600000 gneg
band hs17 q24.3 q24.3 64600000 68400000 gpos75
band hs17 q25.1 q25.1 68400000 72200000 gneg
band hs17 q25.2 q25.2 72200000 72900000 gpos25
band hs17 q25.3 q25.3 72900000 78774742 gneg
band hs18 p11.32 p11.32 0 2900000 gneg
band hs18 p11.31 p11.31 2900000 7200000 gpos50
band hs18 p11.23 p11.23 7200000 8500000 gneg
band hs18 p11.22 p11.22 8500000 10900000 gpos25
band hs18 p11.21 p11.21 10900000 15400000 gneg
band hs18 p11.1 p11.1 15400000 16100000 acen
band hs18 q11.1 q11.1 16100000 17300000 acen
band hs18 q11.2 q11.2 17300000 23300000 gneg
band hs18 q12.1 q12.1 23300000 31000000 gpos100
band hs18 q12.2 q12.2 31000000 35500000 gneg
band hs18 q12.3 q12.3 35500000 41800000 gpos75
band hs18 q21.1 q21.1 41800000 46400000 gneg
band hs18 q21.2 q21.2 46400000 52000000 gpos75
band hs18 q21.31 q21.31 52000000 54400000 gneg
band hs18 q21.32 q21.32 54400000 57100000 gpos50
band hs18 q21.33 q21.33 57100000 59800000 gneg
band hs18 q22.1 q22.1 59800000 64900000 gpos100
band hs18 q22.2 q22.2 64900000 66900000 gneg
band hs18 q22.3 q22.3 66900000 71300000 gpos25
band hs18 q23 q23 71300000 76117153 gneg
band hs19 p13.3 p13.3 0 6900000 gneg
band hs19 p13.2 p13.2 6900000 12600000 gpos25
band hs19 p13.13 p13.13 12600000 13800000 gneg
band hs19 p13.12 p13.12 13800000 16100000 gpos25
band hs19 p13.11 p13.11 16100000 19800000 gneg
band hs19 p12 p12 19800000 26700000 gvar
band hs19 p11 p11 26700000 28500000 acen
band hs19 q11 q11 28500000 30200000 acen
band hs19 q12 q12 30200000 37100000 gvar
band hs19 q13.11 q13.11 37100000 40300000 gneg
band hs19 q13.12 q13.12 40300000 43000000 gpos25
band hs19 q13.13 q13.13 43000000 43400000 gneg
band hs19 q13.2 q13.2 43400000 47800000 gpos25
band hs19 q13.31 q13.31 47800000 50000000 gneg
band hs19 q13.32 q13.32 50000000 53800000 gpos25
band hs19 q13.33 q13.33 53800000 57600000 gneg
band hs19 q13.41 q13.41 57600000 59100000 gpos25
band hs19 q13.42 q13.42 59100000 61400000 gneg
band hs19 q13.43 q13.43 61400000 63811651 gpos25
band hs20 p13 p13 0 5000000 gneg
band hs20 p12.3 p12.3 5000000 9000000 gpos75
band hs20 p12.2 p12.2 9000000 11900000 gneg
band hs20 p12.1 p12.1 11900000 17800000 gpos75
band hs20 p11.23 p11.23 17800000 21200000 gneg
band hs20 p11.22 p11.22 21200000 22300000 gpos25
band hs20 p11.21 p11.21 22300000 25700000 gneg
band hs20 p11.1 p11.1 25700000 27100000 acen
band hs20 q11.1 q11.1 27100000 28400000 acen
band hs20 q11.21 q11.21 28400000 31500000 gneg
band hs20 q11.22 q11.22 31500000 33900000 gpos25
band hs20 q11.23 q11.23 33900000 37100000 gneg
band hs20 q12 q12 37100000 41100000 gpos75
band hs20 q13.11 q13.11 41100000 41600000 gneg
band hs20 q13.12 q13.12 41600000 45800000 gpos25
band hs20 q13.13 q13.13 45800000 49200000 gneg
band hs20 q13.2 q13.2 49200000 54400000 gpos75
band hs20 q13.31 q13.31 54400000 55900000 gneg
band hs20 q13.32 q13.32 55900000 57900000 gpos50
band hs20 q13.33 q13.33 57900000 62435964 gneg
band hs21 p13 p13 0 2900000 gvar
band hs21 p12 p12 2900000 6300000 stalk
band hs21 p11.2 p11.2 6300000 10000000 gvar
band hs21 p11.1 p11.1 10000000 12300000 acen
band hs21 q11.1 q11.1 12300000 13200000 acen
band hs21 q11.2 q11.2 13200000 15300000 gneg
band hs21 q21.1 q21.1 15300000 22900000 gpos100
band hs21 q21.2 q21.2 22900000 25800000 gneg
band hs21 q21.3 q21.3 25800000 30500000 gpos75
band hs21 q22.11 q22.11 30500000 34700000 gneg
band hs21 q22.12 q22.12 34700000 36700000 gpos50
band hs21 q22.13 q22.13 36700000 38600000 gneg
band hs21 q22.2 q22.2 38600000 41400000 gpos50
band hs21 q22.3 q22.3 41400000 46944323 gneg
band hs22 p13 p13 0 3000000 gvar
band hs22 p12 p12 3000000 6600000 stalk
band hs22 p11.2 p11.2 6600000 9600000 gvar
band hs22 p11.1 p11.1 9600000 11800000 acen
band hs22 q11.1 q11.1 11800000 16300000 acen
band hs22 q11.21 q11.21 16300000 20500000 gneg
band hs22 q11.22 q11.22 20500000 21800000 gpos25
band hs22 q11.23 q11.23 21800000 24300000 gneg
band hs22 q12.1 q12.1 24300000 27900000 gpos50
band hs22 q12.2 q12.2 27900000 30500000 gneg
band hs22 q12.3 q12.3 30500000 35900000 gpos50
band hs22 q13.1 q13.1 35900000 39300000 gneg
band hs22 q13.2 q13.2 39300000 42600000 gpos50
band hs22 q13.31 q13.31 42600000 47000000 gneg
band hs22 q13.32 q13.32 47000000 48200000 gpos50
band hs22 q13.33 q13.33 48200000 49691432 gneg

hg19_karyotype_white.txt

Code:

# Human chromsome sizes and cytogenetic band position.
# Data based on hg19/GRCh37 assembly.
chr - hs1 1 0 249250621 white
chr - hs2 2 0 243199373 white
chr - hs3 3 0 198022430 white
chr - hs4 4 0 191154276 white
chr - hs5 5 0 180915260 white
chr - hs6 6 0 171115067 white
chr - hs7 7 0 159138663 white
chr - hs8 8 0 146364022 white
chr - hs9 9 0 141213431 white
chr - hs10 10 0 135534747 white
chr - hs11 11 0 135006516 white
chr - hs12 12 0 133851895 white
chr - hs13 13 0 115169878 white
chr - hs14 14 0 107349540 white
chr - hs15 15 0 102531392 white
chr - hs16 16 0 90354753 white
chr - hs17 17 0 81195210 white
chr - hs18 18 0 78077248 white
chr - hs19 19 0 59128983 white
chr - hs20 20 0 63025520 white
chr - hs21 21 0 48129895 white
chr - hs22 22 0 51304566 white
chr - hsX X 0 155270560 white
chr - hsY Y 0 59373566 white
band hs1 p36.33 p36.33 0 2300000 gneg
band hs1 p36.32 p36.32 2300000 5400000 gpos25
band hs1 p36.31 p36.31 5400000 7200000 gneg
band hs1 p36.23 p36.23 7200000 9200000 gpos25
band hs1 p36.22 p36.22 9200000 12700000 gneg
band hs1 p36.21 p36.21 12700000 16200000 gpos50
band hs1 p36.13 p36.13 16200000 20400000 gneg
band hs1 p36.12 p36.12 20400000 23900000 gpos25
band hs1 p36.11 p36.11 23900000 28000000 gneg
band hs1 p35.3 p35.3 28000000 30200000 gpos25
band hs1 p35.2 p35.2 30200000 32400000 gneg
band hs1 p35.1 p35.1 32400000 34600000 gpos25
band hs1 p34.3 p34.3 34600000 40100000 gneg
band hs1 p34.2 p34.2 40100000 44100000 gpos25
band hs1 p34.1 p34.1 44100000 46800000 gneg
band hs1 p33 p33 46800000 50700000 gpos75
band hs1 p32.3 p32.3 50700000 56100000 gneg
band hs1 p32.2 p32.2 56100000 59000000 gpos50
band hs1 p32.1 p32.1 59000000 61300000 gneg
band hs1 p31.3 p31.3 61300000 68900000 gpos50
band hs1 p31.2 p31.2 68900000 69700000 gneg
band hs1 p31.1 p31.1 69700000 84900000 gpos100
band hs1 p22.3 p22.3 84900000 88400000 gneg
band hs1 p22.2 p22.2 88400000 92000000 gpos75
band hs1 p22.1 p22.1 92000000 94700000 gneg
band hs1 p21.3 p21.3 94700000 99700000 gpos75
band hs1 p21.2 p21.2 99700000 102200000 gneg
band hs1 p21.1 p21.1 102200000 107200000 gpos100
band hs1 p13.3 p13.3 107200000 111800000 gneg
band hs1 p13.2 p13.2 111800000 116100000 gpos50
band hs1 p13.1 p13.1 116100000 117800000 gneg
band hs1 p12 p12 117800000 120600000 gpos50
band hs1 p11.2 p11.2 120600000 121500000 gneg
band hs1 p11.1 p11.1 121500000 125000000 acen
band hs1 q11 q11 125000000 128900000 acen
band hs1 q12 q12 128900000 142600000 gvar
band hs1 q21.1 q21.1 142600000 147000000 gneg
band hs1 q21.2 q21.2 147000000 150300000 gpos50
band hs1 q21.3 q21.3 150300000 155000000 gneg
band hs1 q22 q22 155000000 156500000 gpos50
band hs1 q23.1 q23.1 156500000 159100000 gneg
band hs1 q23.2 q23.2 159100000 160500000 gpos50
band hs1 q23.3 q23.3 160500000 165500000 gneg
band hs1 q24.1 q24.1 165500000 167200000 gpos50
band hs1 q24.2 q24.2 167200000 170900000 gneg
band hs1 q24.3 q24.3 170900000 172900000 gpos75
band hs1 q25.1 q25.1 172900000 176000000 gneg
band hs1 q25.2 q25.2 176000000 180300000 gpos50
band hs1 q25.3 q25.3 180300000 185800000 gneg
band hs1 q31.1 q31.1 185800000 190800000 gpos100
band hs1 q31.2 q31.2 190800000 193800000 gneg
band hs1 q31.3 q31.3 193800000 198700000 gpos100
band hs1 q32.1 q32.1 198700000 207200000 gneg
band hs1 q32.2 q32.2 207200000 211500000 gpos25
band hs1 q32.3 q32.3 211500000 214500000 gneg
band hs1 q41 q41 214500000 224100000 gpos100
band hs1 q42.11 q42.11 224100000 224600000 gneg
band hs1 q42.12 q42.12 224600000 227000000 gpos25
band hs1 q42.13 q42.13 227000000 230700000 gneg
band hs1 q42.2 q42.2 230700000 234700000 gpos50
band hs1 q42.3 q42.3 234700000 236600000 gneg
band hs1 q43 q43 236600000 243700000 gpos75
band hs1 q44 q44 243700000 249250621 gneg
band hs10 p15.3 p15.3 0 3000000 gneg
band hs10 p15.2 p15.2 3000000 3800000 gpos25
band hs10 p15.1 p15.1 3800000 6600000 gneg
band hs10 p14 p14 6600000 12200000 gpos75
band hs10 p13 p13 12200000 17300000 gneg
band hs10 p12.33 p12.33 17300000 18600000 gpos75
band hs10 p12.32 p12.32 18600000 18700000 gneg
band hs10 p12.31 p12.31 18700000 22600000 gpos75
band hs10 p12.2 p12.2 22600000 24600000 gneg
band hs10 p12.1 p12.1 24600000 29600000 gpos50
band hs10 p11.23 p11.23 29600000 31300000 gneg
band hs10 p11.22 p11.22 31300000 34400000 gpos25
band hs10 p11.21 p11.21 34400000 38000000 gneg
band hs10 p11.1 p11.1 38000000 40200000 acen
band hs10 q11.1 q11.1 40200000 42300000 acen
band hs10 q11.21 q11.21 42300000 46100000 gneg
band hs10 q11.22 q11.22 46100000 49900000 gpos25
band hs10 q11.23 q11.23 49900000 52900000 gneg
band hs10 q21.1 q21.1 52900000 61200000 gpos100
band hs10 q21.2 q21.2 61200000 64500000 gneg
band hs10 q21.3 q21.3 64500000 70600000 gpos100
band hs10 q22.1 q22.1 70600000 74900000 gneg
band hs10 q22.2 q22.2 74900000 77700000 gpos50
band hs10 q22.3 q22.3 77700000 82000000 gneg
band hs10 q23.1 q23.1 82000000 87900000 gpos100
band hs10 q23.2 q23.2 87900000 89500000 gneg
band hs10 q23.31 q23.31 89500000 92900000 gpos75
band hs10 q23.32 q23.32 92900000 94100000 gneg
band hs10 q23.33 q23.33 94100000 97000000 gpos50
band hs10 q24.1 q24.1 97000000 99300000 gneg
band hs10 q24.2 q24.2 99300000 101900000 gpos50
band hs10 q24.31 q24.31 101900000 103000000 gneg
band hs10 q24.32 q24.32 103000000 104900000 gpos25
band hs10 q24.33 q24.33 104900000 105800000 gneg
band hs10 q25.1 q25.1 105800000 111900000 gpos100
band hs10 q25.2 q25.2 111900000 114900000 gneg
band hs10 q25.3 q25.3 114900000 119100000 gpos75
band hs10 q26.11 q26.11 119100000 121700000 gneg
band hs10 q26.12 q26.12 121700000 123100000 gpos50
band hs10 q26.13 q26.13 123100000 127500000 gneg
band hs10 q26.2 q26.2 127500000 130600000 gpos50
band hs10 q26.3 q26.3 130600000 135534747 gneg
band hs11 p15.5 p15.5 0 2800000 gneg
band hs11 p15.4 p15.4 2800000 10700000 gpos50
band hs11 p15.3 p15.3 10700000 12700000 gneg
band hs11 p15.2 p15.2 12700000 16200000 gpos50
band hs11 p15.1 p15.1 16200000 21700000 gneg
band hs11 p14.3 p14.3 21700000 26100000 gpos100
band hs11 p14.2 p14.2 26100000 27200000 gneg
band hs11 p14.1 p14.1 27200000 31000000 gpos75
band hs11 p13 p13 31000000 36400000 gneg
band hs11 p12 p12 36400000 43500000 gpos100
band hs11 p11.2 p11.2 43500000 48800000 gneg
band hs11 p11.12 p11.12 48800000 51600000 gpos75
band hs11 p11.11 p11.11 51600000 53700000 acen
band hs11 q11 q11 53700000 55700000 acen
band hs11 q12.1 q12.1 55700000 59900000 gpos75
band hs11 q12.2 q12.2 59900000 61700000 gneg
band hs11 q12.3 q12.3 61700000 63400000 gpos25
band hs11 q13.1 q13.1 63400000 65900000 gneg
band hs11 q13.2 q13.2 65900000 68400000 gpos25
band hs11 q13.3 q13.3 68400000 70400000 gneg
band hs11 q13.4 q13.4 70400000 75200000 gpos50
band hs11 q13.5 q13.5 75200000 77100000 gneg
band hs11 q14.1 q14.1 77100000 85600000 gpos100
band hs11 q14.2 q14.2 85600000 88300000 gneg
band hs11 q14.3 q14.3 88300000 92800000 gpos100
band hs11 q21 q21 92800000 97200000 gneg
band hs11 q22.1 q22.1 97200000 102100000 gpos100
band hs11 q22.2 q22.2 102100000 102900000 gneg
band hs11 q22.3 q22.3 102900000 110400000 gpos100
band hs11 q23.1 q23.1 110400000 112500000 gneg
band hs11 q23.2 q23.2 112500000 114500000 gpos50
band hs11 q23.3 q23.3 114500000 121200000 gneg
band hs11 q24.1 q24.1 121200000 123900000 gpos50
band hs11 q24.2 q24.2 123900000 127800000 gneg
band hs11 q24.3 q24.3 127800000 130800000 gpos50
band hs11 q25 q25 130800000 135006516 gneg
band hs12 p13.33 p13.33 0 3300000 gneg
band hs12 p13.32 p13.32 3300000 5400000 gpos25
band hs12 p13.31 p13.31 5400000 10100000 gneg
band hs12 p13.2 p13.2 10100000 12800000 gpos75
band hs12 p13.1 p13.1 12800000 14800000 gneg
band hs12 p12.3 p12.3 14800000 20000000 gpos100
band hs12 p12.2 p12.2 20000000 21300000 gneg
band hs12 p12.1 p12.1 21300000 26500000 gpos100
band hs12 p11.23 p11.23 26500000 27800000 gneg
band hs12 p11.22 p11.22 27800000 30700000 gpos50
band hs12 p11.21 p11.21 30700000 33300000 gneg
band hs12 p11.1 p11.1 33300000 35800000 acen
band hs12 q11 q11 35800000 38200000 acen
band hs12 q12 q12 38200000 46400000 gpos100
band hs12 q13.11 q13.11 46400000 49100000 gneg
band hs12 q13.12 q13.12 49100000 51500000 gpos25
band hs12 q13.13 q13.13 51500000 54900000 gneg
band hs12 q13.2 q13.2 54900000 56600000 gpos25
band hs12 q13.3 q13.3 56600000 58100000 gneg
band hs12 q14.1 q14.1 58100000 63100000 gpos75
band hs12 q14.2 q14.2 63100000 65100000 gneg
band hs12 q14.3 q14.3 65100000 67700000 gpos50
band hs12 q15 q15 67700000 71500000 gneg
band hs12 q21.1 q21.1 71500000 75700000 gpos75
band hs12 q21.2 q21.2 75700000 80300000 gneg
band hs12 q21.31 q21.31 80300000 86700000 gpos100
band hs12 q21.32 q21.32 86700000 89000000 gneg
band hs12 q21.33 q21.33 89000000 92600000 gpos100
band hs12 q22 q22 92600000 96200000 gneg
band hs12 q23.1 q23.1 96200000 101600000 gpos75
band hs12 q23.2 q23.2 101600000 103800000 gneg
band hs12 q23.3 q23.3 103800000 109000000 gpos50
band hs12 q24.11 q24.11 109000000 111700000 gneg
band hs12 q24.12 q24.12 111700000 112300000 gpos25
band hs12 q24.13 q24.13 112300000 114300000 gneg
band hs12 q24.21 q24.21 114300000 116800000 gpos50
band hs12 q24.22 q24.22 116800000 118100000 gneg
band hs12 q24.23 q24.23 118100000 120700000 gpos50
band hs12 q24.31 q24.31 120700000 125900000 gneg
band hs12 q24.32 q24.32 125900000 129300000 gpos50
band hs12 q24.33 q24.33 129300000 133851895 gneg
band hs13 p13 p13 0 4500000 gvar
band hs13 p12 p12 4500000 10000000 stalk
band hs13 p11.2 p11.2 10000000 16300000 gvar
band hs13 p11.1 p11.1 16300000 17900000 acen
band hs13 q11 q11 17900000 19500000 acen
band hs13 q12.11 q12.11 19500000 23300000 gneg
band hs13 q12.12 q12.12 23300000 25500000 gpos25
band hs13 q12.13 q12.13 25500000 27800000 gneg
band hs13 q12.2 q12.2 27800000 28900000 gpos25
band hs13 q12.3 q12.3 28900000 32200000 gneg
band hs13 q13.1 q13.1 32200000 34000000 gpos50
band hs13 q13.2 q13.2 34000000 35500000 gneg
band hs13 q13.3 q13.3 35500000 40100000 gpos75
band hs13 q14.11 q14.11 40100000 45200000 gneg
band hs13 q14.12 q14.12 45200000 45800000 gpos25
band hs13 q14.13 q14.13 45800000 47300000 gneg
band hs13 q14.2 q14.2 47300000 50900000 gpos50
band hs13 q14.3 q14.3 50900000 55300000 gneg
band hs13 q21.1 q21.1 55300000 59600000 gpos100
band hs13 q21.2 q21.2 59600000 62300000 gneg
band hs13 q21.31 q21.31 62300000 65700000 gpos75
band hs13 q21.32 q21.32 65700000 68600000 gneg
band hs13 q21.33 q21.33 68600000 73300000 gpos100
band hs13 q22.1 q22.1 73300000 75400000 gneg
band hs13 q22.2 q22.2 75400000 77200000 gpos50
band hs13 q22.3 q22.3 77200000 79000000 gneg
band hs13 q31.1 q31.1 79000000 87700000 gpos100
band hs13 q31.2 q31.2 87700000 90000000 gneg
band hs13 q31.3 q31.3 90000000 95000000 gpos100
band hs13 q32.1 q32.1 95000000 98200000 gneg
band hs13 q32.2 q32.2 98200000 99300000 gpos25
band hs13 q32.3 q32.3 99300000 101700000 gneg
band hs13 q33.1 q33.1 101700000 104800000 gpos100
band hs13 q33.2 q33.2 104800000 107000000 gneg
band hs13 q33.3 q33.3 107000000 110300000 gpos100
band hs13 q34 q34 110300000 115169878 gneg
band hs14 p13 p13 0 3700000 gvar
band hs14 p12 p12 3700000 8100000 stalk
band hs14 p11.2 p11.2 8100000 16100000 gvar
band hs14 p11.1 p11.1 16100000 17600000 acen
band hs14 q11.1 q11.1 17600000 19100000 acen
band hs14 q11.2 q11.2 19100000 24600000 gneg
band hs14 q12 q12 24600000 33300000 gpos100
band hs14 q13.1 q13.1 33300000 35300000 gneg
band hs14 q13.2 q13.2 35300000 36600000 gpos50
band hs14 q13.3 q13.3 36600000 37800000 gneg
band hs14 q21.1 q21.1 37800000 43500000 gpos100
band hs14 q21.2 q21.2 43500000 47200000 gneg
band hs14 q21.3 q21.3 47200000 50900000 gpos100
band hs14 q22.1 q22.1 50900000 54100000 gneg
band hs14 q22.2 q22.2 54100000 55500000 gpos25
band hs14 q22.3 q22.3 55500000 58100000 gneg
band hs14 q23.1 q23.1 58100000 62100000 gpos75
band hs14 q23.2 q23.2 62100000 64800000 gneg
band hs14 q23.3 q23.3 64800000 67900000 gpos50
band hs14 q24.1 q24.1 67900000 70200000 gneg
band hs14 q24.2 q24.2 70200000 73800000 gpos50
band hs14 q24.3 q24.3 73800000 79300000 gneg
band hs14 q31.1 q31.1 79300000 83600000 gpos100
band hs14 q31.2 q31.2 83600000 84900000 gneg
band hs14 q31.3 q31.3 84900000 89800000 gpos100
band hs14 q32.11 q32.11 89800000 91900000 gneg
band hs14 q32.12 q32.12 91900000 94700000 gpos25
band hs14 q32.13 q32.13 94700000 96300000 gneg
band hs14 q32.2 q32.2 96300000 101400000 gpos50
band hs14 q32.31 q32.31 101400000 103200000 gneg
band hs14 q32.32 q32.32 103200000 104000000 gpos50
band hs14 q32.33 q32.33 104000000 107349540 gneg
band hs15 p13 p13 0 3900000 gvar
band hs15 p12 p12 3900000 8700000 stalk
band hs15 p11.2 p11.2 8700000 15800000 gvar
band hs15 p11.1 p11.1 15800000 19000000 acen
band hs15 q11.1 q11.1 19000000 20700000 acen
band hs15 q11.2 q11.2 20700000 25700000 gneg
band hs15 q12 q12 25700000 28100000 gpos50
band hs15 q13.1 q13.1 28100000 30300000 gneg
band hs15 q13.2 q13.2 30300000 31200000 gpos50
band hs15 q13.3 q13.3 31200000 33600000 gneg
band hs15 q14 q14 33600000 40100000 gpos75
band hs15 q15.1 q15.1 40100000 42800000 gneg
band hs15 q15.2 q15.2 42800000 43600000 gpos25
band hs15 q15.3 q15.3 43600000 44800000 gneg
band hs15 q21.1 q21.1 44800000 49500000 gpos75
band hs15 q21.2 q21.2 49500000 52900000 gneg
band hs15 q21.3 q21.3 52900000 59100000 gpos75
band hs15 q22.1 q22.1 59100000 59300000 gneg
band hs15 q22.2 q22.2 59300000 63700000 gpos25
band hs15 q22.31 q22.31 63700000 67200000 gneg
band hs15 q22.32 q22.32 67200000 67300000 gpos25
band hs15 q22.33 q22.33 67300000 67500000 gneg
band hs15 q23 q23 67500000 72700000 gpos25
band hs15 q24.1 q24.1 72700000 75200000 gneg
band hs15 q24.2 q24.2 75200000 76600000 gpos25
band hs15 q24.3 q24.3 76600000 78300000 gneg
band hs15 q25.1 q25.1 78300000 81700000 gpos50
band hs15 q25.2 q25.2 81700000 85200000 gneg
band hs15 q25.3 q25.3 85200000 89100000 gpos50
band hs15 q26.1 q26.1 89100000 94300000 gneg
band hs15 q26.2 q26.2 94300000 98500000 gpos50
band hs15 q26.3 q26.3 98500000 102531392 gneg
band hs16 p13.3 p13.3 0 7900000 gneg
band hs16 p13.2 p13.2 7900000 10500000 gpos50
band hs16 p13.13 p13.13 10500000 12600000 gneg
band hs16 p13.12 p13.12 12600000 14800000 gpos50
band hs16 p13.11 p13.11 14800000 16800000 gneg
band hs16 p12.3 p12.3 16800000 21200000 gpos50
band hs16 p12.2 p12.2 21200000 24200000 gneg
band hs16 p12.1 p12.1 24200000 28100000 gpos50
band hs16 p11.2 p11.2 28100000 34600000 gneg
band hs16 p11.1 p11.1 34600000 36600000 acen
band hs16 q11.1 q11.1 36600000 38600000 acen
band hs16 q11.2 q11.2 38600000 47000000 gvar
band hs16 q12.1 q12.1 47000000 52600000 gneg
band hs16 q12.2 q12.2 52600000 56700000 gpos50
band hs16 q13 q13 56700000 57400000 gneg
band hs16 q21 q21 57400000 66700000 gpos100
band hs16 q22.1 q22.1 66700000 70800000 gneg
band hs16 q22.2 q22.2 70800000 72900000 gpos50
band hs16 q22.3 q22.3 72900000 74100000 gneg
band hs16 q23.1 q23.1 74100000 79200000 gpos75
band hs16 q23.2 q23.2 79200000 81700000 gneg
band hs16 q23.3 q23.3 81700000 84200000 gpos50
band hs16 q24.1 q24.1 84200000 87100000 gneg
band hs16 q24.2 q24.2 87100000 88700000 gpos25
band hs16 q24.3 q24.3 88700000 90354753 gneg
band hs17 p13.3 p13.3 0 3300000 gneg
band hs17 p13.2 p13.2 3300000 6500000 gpos50
band hs17 p13.1 p13.1 6500000 10700000 gneg
band hs17 p12 p12 10700000 16000000 gpos75
band hs17 p11.2 p11.2 16000000 22200000 gneg
band hs17 p11.1 p11.1 22200000 24000000 acen
band hs17 q11.1 q11.1 24000000 25800000 acen
band hs17 q11.2 q11.2 25800000 31800000 gneg
band hs17 q12 q12 31800000 38100000 gpos50
band hs17 q21.1 q21.1 38100000 38400000 gneg
band hs17 q21.2 q21.2 38400000 40900000 gpos25
band hs17 q21.31 q21.31 40900000 44900000 gneg
band hs17 q21.32 q21.32 44900000 47400000 gpos25
band hs17 q21.33 q21.33 47400000 50200000 gneg
band hs17 q22 q22 50200000 57600000 gpos75
band hs17 q23.1 q23.1 57600000 58300000 gneg
band hs17 q23.2 q23.2 58300000 61100000 gpos75
band hs17 q23.3 q23.3 61100000 62600000 gneg
band hs17 q24.1 q24.1 62600000 64200000 gpos50
band hs17 q24.2 q24.2 64200000 67100000 gneg
band hs17 q24.3 q24.3 67100000 70900000 gpos75
band hs17 q25.1 q25.1 70900000 74800000 gneg
band hs17 q25.2 q25.2 74800000 75300000 gpos25
band hs17 q25.3 q25.3 75300000 81195210 gneg
band hs18 p11.32 p11.32 0 2900000 gneg
band hs18 p11.31 p11.31 2900000 7100000 gpos50
band hs18 p11.23 p11.23 7100000 8500000 gneg
band hs18 p11.22 p11.22 8500000 10900000 gpos25
band hs18 p11.21 p11.21 10900000 15400000 gneg
band hs18 p11.1 p11.1 15400000 17200000 acen
band hs18 q11.1 q11.1 17200000 19000000 acen
band hs18 q11.2 q11.2 19000000 25000000 gneg
band hs18 q12.1 q12.1 25000000 32700000 gpos100
band hs18 q12.2 q12.2 32700000 37200000 gneg
band hs18 q12.3 q12.3 37200000 43500000 gpos75
band hs18 q21.1 q21.1 43500000 48200000 gneg
band hs18 q21.2 q21.2 48200000 53800000 gpos75
band hs18 q21.31 q21.31 53800000 56200000 gneg
band hs18 q21.32 q21.32 56200000 59000000 gpos50
band hs18 q21.33 q21.33 59000000 61600000 gneg
band hs18 q22.1 q22.1 61600000 66800000 gpos100
band hs18 q22.2 q22.2 66800000 68700000 gneg
band hs18 q22.3 q22.3 68700000 73100000 gpos25
band hs18 q23 q23 73100000 78077248 gneg
band hs19 p13.3 p13.3 0 6900000 gneg
band hs19 p13.2 p13.2 6900000 13900000 gpos25
band hs19 p13.13 p13.13 13900000 14000000 gneg
band hs19 p13.12 p13.12 14000000 16300000 gpos25
band hs19 p13.11 p13.11 16300000 20000000 gneg
band hs19 p12 p12 20000000 24400000 gvar
band hs19 p11 p11 24400000 26500000 acen
band hs19 q11 q11 26500000 28600000 acen
band hs19 q12 q12 28600000 32400000 gvar
band hs19 q13.11 q13.11 32400000 35500000 gneg
band hs19 q13.12 q13.12 35500000 38300000 gpos25
band hs19 q13.13 q13.13 38300000 38700000 gneg
band hs19 q13.2 q13.2 38700000 43400000 gpos25
band hs19 q13.31 q13.31 43400000 45200000 gneg
band hs19 q13.32 q13.32 45200000 48000000 gpos25
band hs19 q13.33 q13.33 48000000 51400000 gneg
band hs19 q13.41 q13.41 51400000 53600000 gpos25
band hs19 q13.42 q13.42 53600000 56300000 gneg
band hs19 q13.43 q13.43 56300000 59128983 gpos25
band hs2 p25.3 p25.3 0 4400000 gneg
band hs2 p25.2 p25.2 4400000 7100000 gpos50
band hs2 p25.1 p25.1 7100000 12200000 gneg
band hs2 p24.3 p24.3 12200000 16700000 gpos75
band hs2 p24.2 p24.2 16700000 19200000 gneg
band hs2 p24.1 p24.1 19200000 24000000 gpos75
band hs2 p23.3 p23.3 24000000 27900000 gneg
band hs2 p23.2 p23.2 27900000 30000000 gpos25
band hs2 p23.1 p23.1 30000000 32100000 gneg
band hs2 p22.3 p22.3 32100000 36600000 gpos75
band hs2 p22.2 p22.2 36600000 38600000 gneg
band hs2 p22.1 p22.1 38600000 41800000 gpos50
band hs2 p21 p21 41800000 47800000 gneg
band hs2 p16.3 p16.3 47800000 52900000 gpos100
band hs2 p16.2 p16.2 52900000 55000000 gneg
band hs2 p16.1 p16.1 55000000 61300000 gpos100
band hs2 p15 p15 61300000 64100000 gneg
band hs2 p14 p14 64100000 68600000 gpos50
band hs2 p13.3 p13.3 68600000 71500000 gneg
band hs2 p13.2 p13.2 71500000 73500000 gpos50
band hs2 p13.1 p13.1 73500000 75000000 gneg
band hs2 p12 p12 75000000 83300000 gpos100
band hs2 p11.2 p11.2 83300000 90500000 gneg
band hs2 p11.1 p11.1 90500000 93300000 acen
band hs2 q11.1 q11.1 93300000 96800000 acen
band hs2 q11.2 q11.2 96800000 102700000 gneg
band hs2 q12.1 q12.1 102700000 106000000 gpos50
band hs2 q12.2 q12.2 106000000 107500000 gneg
band hs2 q12.3 q12.3 107500000 110200000 gpos25
band hs2 q13 q13 110200000 114400000 gneg
band hs2 q14.1 q14.1 114400000 118800000 gpos50
band hs2 q14.2 q14.2 118800000 122400000 gneg
band hs2 q14.3 q14.3 122400000 129900000 gpos50
band hs2 q21.1 q21.1 129900000 132500000 gneg
band hs2 q21.2 q21.2 132500000 135100000 gpos25
band hs2 q21.3 q21.3 135100000 136800000 gneg
band hs2 q22.1 q22.1 136800000 142200000 gpos100
band hs2 q22.2 q22.2 142200000 144100000 gneg
band hs2 q22.3 q22.3 144100000 148700000 gpos100
band hs2 q23.1 q23.1 148700000 149900000 gneg
band hs2 q23.2 q23.2 149900000 150500000 gpos25
band hs2 q23.3 q23.3 150500000 154900000 gneg
band hs2 q24.1 q24.1 154900000 159800000 gpos75
band hs2 q24.2 q24.2 159800000 163700000 gneg
band hs2 q24.3 q24.3 163700000 169700000 gpos75
band hs2 q31.1 q31.1 169700000 178000000 gneg
band hs2 q31.2 q31.2 178000000 180600000 gpos50
band hs2 q31.3 q31.3 180600000 183000000 gneg
band hs2 q32.1 q32.1 183000000 189400000 gpos75
band hs2 q32.2 q32.2 189400000 191900000 gneg
band hs2 q32.3 q32.3 191900000 197400000 gpos75
band hs2 q33.1 q33.1 197400000 203300000 gneg
band hs2 q33.2 q33.2 203300000 204900000 gpos50
band hs2 q33.3 q33.3 204900000 209000000 gneg
band hs2 q34 q34 209000000 215300000 gpos100
band hs2 q35 q35 215300000 221500000 gneg
band hs2 q36.1 q36.1 221500000 225200000 gpos75
band hs2 q36.2 q36.2 225200000 226100000 gneg
band hs2 q36.3 q36.3 226100000 231000000 gpos100
band hs2 q37.1 q37.1 231000000 235600000 gneg
band hs2 q37.2 q37.2 235600000 237300000 gpos50
band hs2 q37.3 q37.3 237300000 243199373 gneg
band hs20 p13 p13 0 5100000 gneg
band hs20 p12.3 p12.3 5100000 9200000 gpos75
band hs20 p12.2 p12.2 9200000 12100000 gneg
band hs20 p12.1 p12.1 12100000 17900000 gpos75
band hs20 p11.23 p11.23 17900000 21300000 gneg
band hs20 p11.22 p11.22 21300000 22300000 gpos25
band hs20 p11.21 p11.21 22300000 25600000 gneg
band hs20 p11.1 p11.1 25600000 27500000 acen
band hs20 q11.1 q11.1 27500000 29400000 acen
band hs20 q11.21 q11.21 29400000 32100000 gneg
band hs20 q11.22 q11.22 32100000 34400000 gpos25
band hs20 q11.23 q11.23 34400000 37600000 gneg
band hs20 q12 q12 37600000 41700000 gpos75
band hs20 q13.11 q13.11 41700000 42100000 gneg
band hs20 q13.12 q13.12 42100000 46400000 gpos25
band hs20 q13.13 q13.13 46400000 49800000 gneg
band hs20 q13.2 q13.2 49800000 55000000 gpos75
band hs20 q13.31 q13.31 55000000 56500000 gneg
band hs20 q13.32 q13.32 56500000 58400000 gpos50
band hs20 q13.33 q13.33 58400000 63025520 gneg
band hs21 p13 p13 0 2800000 gvar
band hs21 p12 p12 2800000 6800000 stalk
band hs21 p11.2 p11.2 6800000 10900000 gvar
band hs21 p11.1 p11.1 10900000 13200000 acen
band hs21 q11.1 q11.1 13200000 14300000 acen
band hs21 q11.2 q11.2 14300000 16400000 gneg
band hs21 q21.1 q21.1 16400000 24000000 gpos100
band hs21 q21.2 q21.2 24000000 26800000 gneg
band hs21 q21.3 q21.3 26800000 31500000 gpos75
band hs21 q22.11 q22.11 31500000 35800000 gneg
band hs21 q22.12 q22.12 35800000 37800000 gpos50
band hs21 q22.13 q22.13 37800000 39700000 gneg
band hs21 q22.2 q22.2 39700000 42600000 gpos50
band hs21 q22.3 q22.3 42600000 48129895 gneg
band hs22 p13 p13 0 3800000 gvar
band hs22 p12 p12 3800000 8300000 stalk
band hs22 p11.2 p11.2 8300000 12200000 gvar
band hs22 p11.1 p11.1 12200000 14700000 acen
band hs22 q11.1 q11.1 14700000 17900000 acen
band hs22 q11.21 q11.21 17900000 22200000 gneg
band hs22 q11.22 q11.22 22200000 23500000 gpos25
band hs22 q11.23 q11.23 23500000 25900000 gneg
band hs22 q12.1 q12.1 25900000 29600000 gpos50
band hs22 q12.2 q12.2 29600000 32200000 gneg
band hs22 q12.3 q12.3 32200000 37600000 gpos50
band hs22 q13.1 q13.1 37600000 41000000 gneg
band hs22 q13.2 q13.2 41000000 44200000 gpos50
band hs22 q13.31 q13.31 44200000 48400000 gneg
band hs22 q13.32 q13.32 48400000 49400000 gpos50
band hs22 q13.33 q13.33 49400000 51304566 gneg
band hs3 p26.3 p26.3 0 2800000 gpos50
band hs3 p26.2 p26.2 2800000 4000000 gneg
band hs3 p26.1 p26.1 4000000 8700000 gpos50
band hs3 p25.3 p25.3 8700000 11800000 gneg
band hs3 p25.2 p25.2 11800000 13300000 gpos25
band hs3 p25.1 p25.1 13300000 16400000 gneg
band hs3 p24.3 p24.3 16400000 23900000 gpos100
band hs3 p24.2 p24.2 23900000 26400000 gneg
band hs3 p24.1 p24.1 26400000 30900000 gpos75
band hs3 p23 p23 30900000 32100000 gneg
band hs3 p22.3 p22.3 32100000 36500000 gpos50
band hs3 p22.2 p22.2 36500000 39400000 gneg
band hs3 p22.1 p22.1 39400000 43700000 gpos75
band hs3 p21.33 p21.33 43700000 44100000 gneg
band hs3 p21.32 p21.32 44100000 44200000 gpos50
band hs3 p21.31 p21.31 44200000 50600000 gneg
band hs3 p21.2 p21.2 50600000 52300000 gpos25
band hs3 p21.1 p21.1 52300000 54400000 gneg
band hs3 p14.3 p14.3 54400000 58600000 gpos50
band hs3 p14.2 p14.2 58600000 63700000 gneg
band hs3 p14.1 p14.1 63700000 69800000 gpos50
band hs3 p13 p13 69800000 74200000 gneg
band hs3 p12.3 p12.3 74200000 79800000 gpos75
band hs3 p12.2 p12.2 79800000 83500000 gneg
band hs3 p12.1 p12.1 83500000 87200000 gpos75
band hs3 p11.2 p11.2 87200000 87900000 gneg
band hs3 p11.1 p11.1 87900000 91000000 acen
band hs3 q11.1 q11.1 91000000 93900000 acen
band hs3 q11.2 q11.2 93900000 98300000 gvar
band hs3 q12.1 q12.1 98300000 100000000 gneg
band hs3 q12.2 q12.2 100000000 100900000 gpos25
band hs3 q12.3 q12.3 100900000 102800000 gneg
band hs3 q13.11 q13.11 102800000 106200000 gpos75
band hs3 q13.12 q13.12 106200000 107900000 gneg
band hs3 q13.13 q13.13 107900000 111300000 gpos50
band hs3 q13.2 q13.2 111300000 113500000 gneg
band hs3 q13.31 q13.31 113500000 117300000 gpos75
band hs3 q13.32 q13.32 117300000 119000000 gneg
band hs3 q13.33 q13.33 119000000 121900000 gpos75
band hs3 q21.1 q21.1 121900000 123800000 gneg
band hs3 q21.2 q21.2 123800000 125800000 gpos25
band hs3 q21.3 q21.3 125800000 129200000 gneg
band hs3 q22.1 q22.1 129200000 133700000 gpos25
band hs3 q22.2 q22.2 133700000 135700000 gneg
band hs3 q22.3 q22.3 135700000 138700000 gpos25
band hs3 q23 q23 138700000 142800000 gneg
band hs3 q24 q24 142800000 148900000 gpos100
band hs3 q25.1 q25.1 148900000 152100000 gneg
band hs3 q25.2 q25.2 152100000 155000000 gpos50
band hs3 q25.31 q25.31 155000000 157000000 gneg
band hs3 q25.32 q25.32 157000000 159000000 gpos50
band hs3 q25.33 q25.33 159000000 160700000 gneg
band hs3 q26.1 q26.1 160700000 167600000 gpos100
band hs3 q26.2 q26.2 167600000 170900000 gneg
band hs3 q26.31 q26.31 170900000 175700000 gpos75
band hs3 q26.32 q26.32 175700000 179000000 gneg
band hs3 q26.33 q26.33 179000000 182700000 gpos75
band hs3 q27.1 q27.1 182700000 184500000 gneg
band hs3 q27.2 q27.2 184500000 186000000 gpos25
band hs3 q27.3 q27.3 186000000 187900000 gneg
band hs3 q28 q28 187900000 192300000 gpos75
band hs3 q29 q29 192300000 198022430 gneg
band hs4 p16.3 p16.3 0 4500000 gneg
band hs4 p16.2 p16.2 4500000 6000000 gpos25
band hs4 p16.1 p16.1 6000000 11300000 gneg
band hs4 p15.33 p15.33 11300000 15200000 gpos50
band hs4 p15.32 p15.32 15200000 17800000 gneg
band hs4 p15.31 p15.31 17800000 21300000 gpos75
band hs4 p15.2 p15.2 21300000 27700000 gneg
band hs4 p15.1 p15.1 27700000 35800000 gpos100
band hs4 p14 p14 35800000 41200000 gneg
band hs4 p13 p13 41200000 44600000 gpos50
band hs4 p12 p12 44600000 48200000 gneg
band hs4 p11 p11 48200000 50400000 acen
band hs4 q11 q11 50400000 52700000 acen
band hs4 q12 q12 52700000 59500000 gneg
band hs4 q13.1 q13.1 59500000 66600000 gpos100
band hs4 q13.2 q13.2 66600000 70500000 gneg
band hs4 q13.3 q13.3 70500000 76300000 gpos75
band hs4 q21.1 q21.1 76300000 78900000 gneg
band hs4 q21.21 q21.21 78900000 82400000 gpos50
band hs4 q21.22 q21.22 82400000 84100000 gneg
band hs4 q21.23 q21.23 84100000 86900000 gpos25
band hs4 q21.3 q21.3 86900000 88000000 gneg
band hs4 q22.1 q22.1 88000000 93700000 gpos75
band hs4 q22.2 q22.2 93700000 95100000 gneg
band hs4 q22.3 q22.3 95100000 98800000 gpos75
band hs4 q23 q23 98800000 101100000 gneg
band hs4 q24 q24 101100000 107700000 gpos50
band hs4 q25 q25 107700000 114100000 gneg
band hs4 q26 q26 114100000 120800000 gpos75
band hs4 q27 q27 120800000 123800000 gneg
band hs4 q28.1 q28.1 123800000 128800000 gpos50
band hs4 q28.2 q28.2 128800000 131100000 gneg
band hs4 q28.3 q28.3 131100000 139500000 gpos100
band hs4 q31.1 q31.1 139500000 141500000 gneg
band hs4 q31.21 q31.21 141500000 146800000 gpos25
band hs4 q31.22 q31.22 146800000 148500000 gneg
band hs4 q31.23 q31.23 148500000 151100000 gpos25
band hs4 q31.3 q31.3 151100000 155600000 gneg
band hs4 q32.1 q32.1 155600000 161800000 gpos100
band hs4 q32.2 q32.2 161800000 164500000 gneg
band hs4 q32.3 q32.3 164500000 170100000 gpos100
band hs4 q33 q33 170100000 171900000 gneg
band hs4 q34.1 q34.1 171900000 176300000 gpos75
band hs4 q34.2 q34.2 176300000 177500000 gneg
band hs4 q34.3 q34.3 177500000 183200000 gpos100
band hs4 q35.1 q35.1 183200000 187100000 gneg
band hs4 q35.2 q35.2 187100000 191154276 gpos25
band hs5 p15.33 p15.33 0 4500000 gneg
band hs5 p15.32 p15.32 4500000 6300000 gpos25
band hs5 p15.31 p15.31 6300000 9800000 gneg
band hs5 p15.2 p15.2 9800000 15000000 gpos50
band hs5 p15.1 p15.1 15000000 18400000 gneg
band hs5 p14.3 p14.3 18400000 23300000 gpos100
band hs5 p14.2 p14.2 23300000 24600000 gneg
band hs5 p14.1 p14.1 24600000 28900000 gpos100
band hs5 p13.3 p13.3 28900000 33800000 gneg
band hs5 p13.2 p13.2 33800000 38400000 gpos25
band hs5 p13.1 p13.1 38400000 42500000 gneg
band hs5 p12 p12 42500000 46100000 gpos50
band hs5 p11 p11 46100000 48400000 acen
band hs5 q11.1 q11.1 48400000 50700000 acen
band hs5 q11.2 q11.2 50700000 58900000 gneg
band hs5 q12.1 q12.1 58900000 62900000 gpos75
band hs5 q12.2 q12.2 62900000 63200000 gneg
band hs5 q12.3 q12.3 63200000 66700000 gpos75
band hs5 q13.1 q13.1 66700000 68400000 gneg
band hs5 q13.2 q13.2 68400000 73300000 gpos50
band hs5 q13.3 q13.3 73300000 76900000 gneg
band hs5 q14.1 q14.1 76900000 81400000 gpos50
band hs5 q14.2 q14.2 81400000 82800000 gneg
band hs5 q14.3 q14.3 82800000 92300000 gpos100
band hs5 q15 q15 92300000 98200000 gneg
band hs5 q21.1 q21.1 98200000 102800000 gpos100
band hs5 q21.2 q21.2 102800000 104500000 gneg
band hs5 q21.3 q21.3 104500000 109600000 gpos100
band hs5 q22.1 q22.1 109600000 111500000 gneg
band hs5 q22.2 q22.2 111500000 113100000 gpos50
band hs5 q22.3 q22.3 113100000 115200000 gneg
band hs5 q23.1 q23.1 115200000 121400000 gpos100
band hs5 q23.2 q23.2 121400000 127300000 gneg
band hs5 q23.3 q23.3 127300000 130600000 gpos100
band hs5 q31.1 q31.1 130600000 136200000 gneg
band hs5 q31.2 q31.2 136200000 139500000 gpos25
band hs5 q31.3 q31.3 139500000 144500000 gneg
band hs5 q32 q32 144500000 149800000 gpos75
band hs5 q33.1 q33.1 149800000 152700000 gneg
band hs5 q33.2 q33.2 152700000 155700000 gpos50
band hs5 q33.3 q33.3 155700000 159900000 gneg
band hs5 q34 q34 159900000 168500000 gpos100
band hs5 q35.1 q35.1 168500000 172800000 gneg
band hs5 q35.2 q35.2 172800000 176600000 gpos25
band hs5 q35.3 q35.3 176600000 180915260 gneg
band hs6 p25.3 p25.3 0 2300000 gneg
band hs6 p25.2 p25.2 2300000 4200000 gpos25
band hs6 p25.1 p25.1 4200000 7100000 gneg
band hs6 p24.3 p24.3 7100000 10600000 gpos50
band hs6 p24.2 p24.2 10600000 11600000 gneg
band hs6 p24.1 p24.1 11600000 13400000 gpos25
band hs6 p23 p23 13400000 15200000 gneg
band hs6 p22.3 p22.3 15200000 25200000 gpos75
band hs6 p22.2 p22.2 25200000 27000000 gneg
band hs6 p22.1 p22.1 27000000 30400000 gpos50
band hs6 p21.33 p21.33 30400000 32100000 gneg
band hs6 p21.32 p21.32 32100000 33500000 gpos25
band hs6 p21.31 p21.31 33500000 36600000 gneg
band hs6 p21.2 p21.2 36600000 40500000 gpos25
band hs6 p21.1 p21.1 40500000 46200000 gneg
band hs6 p12.3 p12.3 46200000 51800000 gpos100
band hs6 p12.2 p12.2 51800000 52900000 gneg
band hs6 p12.1 p12.1 52900000 57000000 gpos100
band hs6 p11.2 p11.2 57000000 58700000 gneg
band hs6 p11.1 p11.1 58700000 61000000 acen
band hs6 q11.1 q11.1 61000000 63300000 acen
band hs6 q11.2 q11.2 63300000 63400000 gneg
band hs6 q12 q12 63400000 70000000 gpos100
band hs6 q13 q13 70000000 75900000 gneg
band hs6 q14.1 q14.1 75900000 83900000 gpos50
band hs6 q14.2 q14.2 83900000 84900000 gneg
band hs6 q14.3 q14.3 84900000 88000000 gpos50
band hs6 q15 q15 88000000 93100000 gneg
band hs6 q16.1 q16.1 93100000 99500000 gpos100
band hs6 q16.2 q16.2 99500000 100600000 gneg
band hs6 q16.3 q16.3 100600000 105500000 gpos100
band hs6 q21 q21 105500000 114600000 gneg
band hs6 q22.1 q22.1 114600000 118300000 gpos75
band hs6 q22.2 q22.2 118300000 118500000 gneg
band hs6 q22.31 q22.31 118500000 126100000 gpos100
band hs6 q22.32 q22.32 126100000 127100000 gneg
band hs6 q22.33 q22.33 127100000 130300000 gpos75
band hs6 q23.1 q23.1 130300000 131200000 gneg
band hs6 q23.2 q23.2 131200000 135200000 gpos50
band hs6 q23.3 q23.3 135200000 139000000 gneg
band hs6 q24.1 q24.1 139000000 142800000 gpos75
band hs6 q24.2 q24.2 142800000 145600000 gneg
band hs6 q24.3 q24.3 145600000 149000000 gpos75
band hs6 q25.1 q25.1 149000000 152500000 gneg
band hs6 q25.2 q25.2 152500000 155500000 gpos50
band hs6 q25.3 q25.3 155500000 161000000 gneg
band hs6 q26 q26 161000000 164500000 gpos50
band hs6 q27 q27 164500000 171115067 gneg
band hs7 p22.3 p22.3 0 2800000 gneg
band hs7 p22.2 p22.2 2800000 4500000 gpos25
band hs7 p22.1 p22.1 4500000 7300000 gneg
band hs7 p21.3 p21.3 7300000 13800000 gpos100
band hs7 p21.2 p21.2 13800000 16500000 gneg
band hs7 p21.1 p21.1 16500000 20900000 gpos100
band hs7 p15.3 p15.3 20900000 25500000 gneg
band hs7 p15.2 p15.2 25500000 28000000 gpos50
band hs7 p15.1 p15.1 28000000 28800000 gneg
band hs7 p14.3 p14.3 28800000 35000000 gpos75
band hs7 p14.2 p14.2 35000000 37200000 gneg
band hs7 p14.1 p14.1 37200000 43300000 gpos75
band hs7 p13 p13 43300000 45400000 gneg
band hs7 p12.3 p12.3 45400000 49000000 gpos75
band hs7 p12.2 p12.2 49000000 50500000 gneg
band hs7 p12.1 p12.1 50500000 54000000 gpos75
band hs7 p11.2 p11.2 54000000 58000000 gneg
band hs7 p11.1 p11.1 58000000 59900000 acen
band hs7 q11.1 q11.1 59900000 61700000 acen
band hs7 q11.21 q11.21 61700000 67000000 gneg
band hs7 q11.22 q11.22 67000000 72200000 gpos50
band hs7 q11.23 q11.23 72200000 77500000 gneg
band hs7 q21.11 q21.11 77500000 86400000 gpos100
band hs7 q21.12 q21.12 86400000 88200000 gneg
band hs7 q21.13 q21.13 88200000 91100000 gpos75
band hs7 q21.2 q21.2 91100000 92800000 gneg
band hs7 q21.3 q21.3 92800000 98000000 gpos75
band hs7 q22.1 q22.1 98000000 103800000 gneg
band hs7 q22.2 q22.2 103800000 104500000 gpos50
band hs7 q22.3 q22.3 104500000 107400000 gneg
band hs7 q31.1 q31.1 107400000 114600000 gpos75
band hs7 q31.2 q31.2 114600000 117400000 gneg
band hs7 q31.31 q31.31 117400000 121100000 gpos75
band hs7 q31.32 q31.32 121100000 123800000 gneg
band hs7 q31.33 q31.33 123800000 127100000 gpos75
band hs7 q32.1 q32.1 127100000 129200000 gneg
band hs7 q32.2 q32.2 129200000 130400000 gpos25
band hs7 q32.3 q32.3 130400000 132600000 gneg
band hs7 q33 q33 132600000 138200000 gpos50
band hs7 q34 q34 138200000 143100000 gneg
band hs7 q35 q35 143100000 147900000 gpos75
band hs7 q36.1 q36.1 147900000 152600000 gneg
band hs7 q36.2 q36.2 152600000 155100000 gpos25
band hs7 q36.3 q36.3 155100000 159138663 gneg
band hs8 p23.3 p23.3 0 2200000 gneg
band hs8 p23.2 p23.2 2200000 6200000 gpos75
band hs8 p23.1 p23.1 6200000 12700000 gneg
band hs8 p22 p22 12700000 19000000 gpos100
band hs8 p21.3 p21.3 19000000 23300000 gneg
band hs8 p21.2 p21.2 23300000 27400000 gpos50
band hs8 p21.1 p21.1 27400000 28800000 gneg
band hs8 p12 p12 28800000 36500000 gpos75
band hs8 p11.23 p11.23 36500000 38300000 gneg
band hs8 p11.22 p11.22 38300000 39700000 gpos25
band hs8 p11.21 p11.21 39700000 43100000 gneg
band hs8 p11.1 p11.1 43100000 45600000 acen
band hs8 q11.1 q11.1 45600000 48100000 acen
band hs8 q11.21 q11.21 48100000 52200000 gneg
band hs8 q11.22 q11.22 52200000 52600000 gpos75
band hs8 q11.23 q11.23 52600000 55500000 gneg
band hs8 q12.1 q12.1 55500000 61600000 gpos50
band hs8 q12.2 q12.2 61600000 62200000 gneg
band hs8 q12.3 q12.3 62200000 66000000 gpos50
band hs8 q13.1 q13.1 66000000 68000000 gneg
band hs8 q13.2 q13.2 68000000 70500000 gpos50
band hs8 q13.3 q13.3 70500000 73900000 gneg
band hs8 q21.11 q21.11 73900000 78300000 gpos100
band hs8 q21.12 q21.12 78300000 80100000 gneg
band hs8 q21.13 q21.13 80100000 84600000 gpos75
band hs8 q21.2 q21.2 84600000 86900000 gneg
band hs8 q21.3 q21.3 86900000 93300000 gpos100
band hs8 q22.1 q22.1 93300000 99000000 gneg
band hs8 q22.2 q22.2 99000000 101600000 gpos25
band hs8 q22.3 q22.3 101600000 106200000 gneg
band hs8 q23.1 q23.1 106200000 110500000 gpos75
band hs8 q23.2 q23.2 110500000 112100000 gneg
band hs8 q23.3 q23.3 112100000 117700000 gpos100
band hs8 q24.11 q24.11 117700000 119200000 gneg
band hs8 q24.12 q24.12 119200000 122500000 gpos50
band hs8 q24.13 q24.13 122500000 127300000 gneg
band hs8 q24.21 q24.21 127300000 131500000 gpos50
band hs8 q24.22 q24.22 131500000 136400000 gneg
band hs8 q24.23 q24.23 136400000 139900000 gpos75
band hs8 q24.3 q24.3 139900000 146364022 gneg
band hs9 p24.3 p24.3 0 2200000 gneg
band hs9 p24.2 p24.2 2200000 4600000 gpos25
band hs9 p24.1 p24.1 4600000 9000000 gneg
band hs9 p23 p23 9000000 14200000 gpos75
band hs9 p22.3 p22.3 14200000 16600000 gneg
band hs9 p22.2 p22.2 16600000 18500000 gpos25
band hs9 p22.1 p22.1 18500000 19900000 gneg
band hs9 p21.3 p21.3 19900000 25600000 gpos100
band hs9 p21.2 p21.2 25600000 28000000 gneg
band hs9 p21.1 p21.1 28000000 33200000 gpos100
band hs9 p13.3 p13.3 33200000 36300000 gneg
band hs9 p13.2 p13.2 36300000 38400000 gpos25
band hs9 p13.1 p13.1 38400000 41000000 gneg
band hs9 p12 p12 41000000 43600000 gpos50
band hs9 p11.2 p11.2 43600000 47300000 gneg
band hs9 p11.1 p11.1 47300000 49000000 acen
band hs9 q11 q11 49000000 50700000 acen
band hs9 q12 q12 50700000 65900000 gvar
band hs9 q13 q13 65900000 68700000 gneg
band hs9 q21.11 q21.11 68700000 72200000 gpos25
band hs9 q21.12 q21.12 72200000 74000000 gneg
band hs9 q21.13 q21.13 74000000 79200000 gpos50
band hs9 q21.2 q21.2 79200000 81100000 gneg
band hs9 q21.31 q21.31 81100000 84100000 gpos50
band hs9 q21.32 q21.32 84100000 86900000 gneg
band hs9 q21.33 q21.33 86900000 90400000 gpos50
band hs9 q22.1 q22.1 90400000 91800000 gneg
band hs9 q22.2 q22.2 91800000 93900000 gpos25
band hs9 q22.31 q22.31 93900000 96600000 gneg
band hs9 q22.32 q22.32 96600000 99300000 gpos25
band hs9 q22.33 q22.33 99300000 102600000 gneg
band hs9 q31.1 q31.1 102600000 108200000 gpos100
band hs9 q31.2 q31.2 108200000 111300000 gneg
band hs9 q31.3 q31.3 111300000 114900000 gpos25
band hs9 q32 q32 114900000 117700000 gneg
band hs9 q33.1 q33.1 117700000 122500000 gpos75
band hs9 q33.2 q33.2 122500000 125800000 gneg
band hs9 q33.3 q33.3 125800000 130300000 gpos25
band hs9 q34.11 q34.11 130300000 133500000 gneg
band hs9 q34.12 q34.12 133500000 134000000 gpos25
band hs9 q34.13 q34.13 134000000 135900000 gneg
band hs9 q34.2 q34.2 135900000 137400000 gpos25
band hs9 q34.3 q34.3 137400000 141213431 gneg
band hsX p22.33 p22.33 0 4300000 gneg
band hsX p22.32 p22.32 4300000 6000000 gpos50
band hsX p22.31 p22.31 6000000 9500000 gneg
band hsX p22.2 p22.2 9500000 17100000 gpos50
band hsX p22.13 p22.13 17100000 19300000 gneg
band hsX p22.12 p22.12 19300000 21900000 gpos50
band hsX p22.11 p22.11 21900000 24900000 gneg
band hsX p21.3 p21.3 24900000 29300000 gpos100
band hsX p21.2 p21.2 29300000 31500000 gneg
band hsX p21.1 p21.1 31500000 37600000 gpos100
band hsX p11.4 p11.4 37600000 42400000 gneg
band hsX p11.3 p11.3 42400000 46400000 gpos75
band hsX p11.23 p11.23 46400000 49800000 gneg
band hsX p11.22 p11.22 49800000 54800000 gpos25
band hsX p11.21 p11.21 54800000 58100000 gneg
band hsX p11.1 p11.1 58100000 60600000 acen
band hsX q11.1 q11.1 60600000 63000000 acen
band hsX q11.2 q11.2 63000000 64600000 gneg
band hsX q12 q12 64600000 67800000 gpos50
band hsX q13.1 q13.1 67800000 71800000 gneg
band hsX q13.2 q13.2 71800000 73900000 gpos50
band hsX q13.3 q13.3 73900000 76000000 gneg
band hsX q21.1 q21.1 76000000 84600000 gpos100
band hsX q21.2 q21.2 84600000 86200000 gneg
band hsX q21.31 q21.31 86200000 91800000 gpos100
band hsX q21.32 q21.32 91800000 93500000 gneg
band hsX q21.33 q21.33 93500000 98300000 gpos75
band hsX q22.1 q22.1 98300000 102600000 gneg
band hsX q22.2 q22.2 102600000 103700000 gpos50
band hsX q22.3 q22.3 103700000 108700000 gneg
band hsX q23 q23 108700000 116500000 gpos75
band hsX q24 q24 116500000 120900000 gneg
band hsX q25 q25 120900000 128700000 gpos100
band hsX q26.1 q26.1 128700000 130400000 gneg
band hsX q26.2 q26.2 130400000 133600000 gpos25
band hsX q26.3 q26.3 133600000 138000000 gneg
band hsX q27.1 q27.1 138000000 140300000 gpos75
band hsX q27.2 q27.2 140300000 142100000 gneg
band hsX q27.3 q27.3 142100000 147100000 gpos100
band hsX q28 q28 147100000 155270560 gneg
band hsY p11.32 p11.32 0 2500000 gneg
band hsY p11.31 p11.31 2500000 3000000 gpos50
band hsY p11.2 p11.2 3000000 11600000 gneg
band hsY p11.1 p11.1 11600000 12500000 acen
band hsY q11.1 q11.1 12500000 13400000 acen
band hsY q11.21 q11.21 13400000 15100000 gneg
band hsY q11.221 q11.221 15100000 19800000 gpos50
band hsY q11.222 q11.222 19800000 22100000 gneg
band hsY q11.223 q11.223 22100000 26200000 gpos50
band hsY q11.23 q11.23 26200000 28800000 gneg
band hsY q12 q12 28800000 59373566 gvar

my_colors.conf

Code:

# RGB color definition. Colors are refered to within configuration files
# by their name. In order to use a color, you must define it here. 
# 
# e.g. if you really must use 'bisque', then add
#
# bisque = 255,228,196
#
# Many useful colors are already defined. In general, given a HUE, these
# colors are defined
#
# vlHUE (very light HUE, e.g. vlred)
# lHUE  (light HUE, e.g. red)
# HUE   (e.g. red)
# dHUE  (dark HUE, e.g. dred)
#
# In addition to hues, two other color groups are defined. 
#
# - cytogenetic band colors (e.g. gposNNN, acen, stalk, etc.) which
#   correspond to colors on ideogram bands
# - UCSC chromosome color palette (e.g. chrNN, chrUn, chrNA)

optblue   = 55,133,221
optgreen  = 55,221,125
optyellow = 221,215,55
optorange = 221,164,55
optred    = 221,55,55
optviolet = 145,55,221
optpurple = 219,55,221

white     = 255,255,255
vvvvlgrey = 250,250,250
vvvlgrey  = 240,240,240
vvlgrey   = 230,230,230
vlgrey    = 220,220,220
lgrey     = 210,210,210
grey      = 200,200,200
dgrey     = 170,170,170
vdgrey    = 140,140,140
vvdgrey   = 100,100,100
vvvdgrey  = 70,70,70
vvvvdgrey = 40,40,40
black     = 0,0,0

vlred   = 255,193,200
lred    = 255,122,137
red     = 247,42,66
pred	= 255,0.0
dred    = 205,51,69

vlgreen = 204,255,218
lgreen  = 128,255,164
green   = 51,204,94
pgreen	= 0,255,0
dgreen  = 38,153,71

vlblue  = 128,176,255
lblue   = 64,137,255
blue    = 54,116,217
pblue	= 0,0,255
dblue   = 38,82,153

vlpurple= 242,128,255
lpurple = 236,64,255
purple  = 189,51,204
dpurple = 118,32,128

vlyellow = 255,253,202
lyellow  = 255,252,150
yellow   = 255,255,0
dyellow  = 191,186,48

lime     = 186,255,0

vlorange = 255,228,193
lorange  = 255,187,110
orange   = 255,136,0
dorange  = 221,143,55

# karyotype colors

gpos100 = 0,0,0
gpos    = 0,0,0
gpos75  = 130,130,130
gpos66  = 160,160,160
gpos50  = 200,200,200
gpos33  = 210,210,210
gpos25  = 200,200,200
gvar    = 220,220,220
gneg    = 255,255,255
acen    = 217,47,39
stalk   = 100,127,164

# others

select = 135,177,255

# new york times cmyk-safe

# roygbiv - normal
nyt_blue   = 104,152,178
nyt_green  = 137,129,96
nyt_yellow = 241,221,117
nyt_orange = 230,146,57
nyt_red    = 217,47,39

# chromosome color map (UCSC) 

chr1 = 153,102,0
chr2 = 102,102,0
chr3 = 153,153,30
chr4 = 204,0,0
chr5 = 255,0,0
chr6 = 255,0,204
chr7 = 255,204,204
chr8 = 255,153,0
chr9 = 255,204,0
chr10 = 255,255,0
chr11 = 204,255,0
chr12 = 0,255,0
chr13 = 53,128,0
chr14 = 0,0,204
chr15 = 102,153,255
chr16 = 153,204,255
chr17 = 0,255,255
chr18 = 204,255,255
chr19 = 153,0,204
chr20 = 204,51,255
chr21 = 204,153,255
chr22 = 102,102,102
chr23 = 153,153,153
chrX  = 153,153,153
chr24 = 204,204,204
chrY = 204,204,204
chrM = 204,204,153
chr0 = 204,204,153
chrUn = 121,204,61
chrNA = 255,255,255

# 11 intensity range three color palette defined from http://colorbrewer2.org used for heatmaps

jk1 = 0,104,55
jk2 = 26,152,80
jk3 = 102,189,99
jk4 = 166,217,106
jk5 = 217,239,139
jk6 = 255,255,191
jk7 = 254,224,139
jk8 = 253,174,97
jk9 = 244,109,67
jk10 = 213,62,79
jk11 = 158,1,66

my_ideogram.txt

Code:

<ideogram>

<spacing>

default = 10u

</spacing>

# thickness (px) of chromosome ideogram
thickness        = 100p
stroke_thickness = 2
# ideogram border color
stroke_color     = black
fill             = yes
# the default chromosome color is set here and any value
# defined in the karyotype file overrides it
fill_color       = black

# fractional radius position of chromosome ideogram within image
radius         = 0.85r
show_label     = yes
label_font     = condensedbold
label_radius   = dims(ideogram,radius) + 0.03r
# Original label_radius   = dims(ideogram,radius) + 0.05r
label_size     = 28
# Original label_size     = 16
label_parallel = no

# cytogenetic bands
band_stroke_thickness = 1

# show_bands determines whether the outline of cytogenetic bands
# will be seen
show_bands            = yes
# in order to fill the bands with the color defined in the karyotype
# file you must set fill_bands
fill_bands            = yes

band_transparency     = 1

</ideogram>

my_ticks.conf

Code:

show_ticks          = yes
show_tick_labels    = yes

grid_start         = dims(ideogram,radius_inner)-0.5r
grid_end           = dims(ideogram,radius_outer)+100

<ticks>
skip_first_label     = no
skip_last_label      = no
radius               = dims(ideogram,radius_outer)
tick_separation      = 2p
min_label_distance_to_edge = 0p
label_separation = 5p
label_offset     = 2p
label_size = 8p
multiplier = 1e-6
color = black

<tick>
spacing        = 5u
size           = 5p
thickness      = 2p
color          = black
show_label     = no
label_size     = 8p
label_offset   = 0p
format         = %d
grid           = yes
grid_color     = grey
grid_thickness = 1p
</tick>
<tick>
spacing        = 25u
size           = 8p
thickness      = 2p
color          = black
show_label     = yes
label_size     = 12p
label_offset   = 0p
format         = %d
grid           = yes
grid_color     = dgrey
grid_thickness = 1p
</tick>
</ticks>

I'll try to post a copy of a configuration file and some simple data tables that can be used to generate a basic plot with the features most people on this forum would be interested in plotting in the coming days.

**ECO** · 02-14-2011, 09:17 AM

Jon,

Another great post. I spent a ton of time getting circos to "tutorial phase". Would you mind if I broke this circos post out into its own thread?

**nilshomer** · 02-14-2011, 09:56 AM

There are a lot of circos whizzes on this site, so do not hesitate to ask questions! I agree with echo about making a dedicated circos thread.

**Jon_Keats** · 02-14-2011, 11:26 PM

A Circos Example

***A Simple Example from the Multiple Myeloma World***

1) Place this configuration file in the "my_config_files" folder

myeloma_circos.conf

Code:

############################################################
## Common Layout Settings
############################################################

## Defines color names you can reference in tables and configuration and there associated RGB values
<colors>
<<include my_reference_files/my_colors.conf>>
</colors>

## Defines font names you can reference in tables and configuration files
<fonts>
<<include etc/fonts.conf>>
</fonts>

## Defines ideogram mapping characteristics
<<include my_reference_files/my_ideogram.conf>>

## Defines ideogram tick mapping characteristics
<<include my_reference_files/my_ticks.conf>>

############################################################
## General Plot Settings
############################################################

## Define karyotype file name and location to be used in this plot
karyotype   = my_reference_files/hg18_karyotype_white.txt

<image>
## Define output directory (command line over-ride with: -outputdir /path/to/your/output/directory)
dir = my_plots

## Define output file name (command line over-ride with: -outputfile your_image_name.png)
file  = myeloma_example.png

## Define output file types
png = yes
svg = yes

## Define size of image (radius of inscribed circle in image)
radius         = 1500p

## Define background color of image (color name must be in your colors.conf file)
background     = white

## Define the angle at which to start rendering the image (by default angle=0 is at 3 o'clock position)
angle_offset   = -90

24bit = yes
auto_alpha_colors = yes
auto_alpha_steps  = 5

</image>

chromosomes_units = 1000000
chromosomes_display_default = yes

############################################################
## Specific Plot Settings
############################################################

<plots>

############################################################
## Heatmap Plot ##

<plot>

type	= heatmap
color	= jk1,jk2,jk3,jk4,jk5,jk6,jk7,jk8,jk9,jk10,jk11
min	= -3
max	= 3
file	= my_data_files/heatmap.txt
r0	= 0.92r
r1	= 0.98r

</plot>

############################################################
## Scatter Plot ##

<plot>

show  = yes
type  = scatter
file  = my_data_files/scatter.txt
fill_color = jk6
stroke_color     = jk6
stroke_thickness = 1
glyph = circle
glyph_size = 3
min   = -5
max   = 5
r0    = 0.78r
r1    = 0.90r

background       = yes
background_color = vlgrey
#background_stroke_color = black
#background_stroke_thickness = 1

axis           = yes
axis_color     = dgrey
axis_thickness = 1
axis_spacing   = 1.0

<rules>

<rule>
importance   = 100
condition    = _VALUE_ < -4
stroke_color = jk1
fill_color   = jk1
glyph        = circle
glyph_size = 10
</rule>

<rule>
importance   = 95
condition    = _VALUE_ < -3
stroke_color = jk2
fill_color   = jk2
glyph        = circle
glyph_size = 8.5
</rule>

<rule>
importance   = 90
condition    = _VALUE_ < -2.5
stroke_color = jk3
fill_color   = jk3
glyph        = circle
glyph_size = 7
</rule>

<rule>
importance   = 85
condition    = _VALUE_ < -2
stroke_color = jk4
fill_color   = jk4
glyph        = circle
glyph_size = 5.5
</rule>

<rule>
importance   = 80
condition    = _VALUE_ < -1
stroke_color = jk5
fill_color   = jk5
glyph        = circle
glyph_size = 4
</rule>

<rule>
importance   = 80
condition    = _VALUE_ > 1
stroke_color = jk7
fill_color   = jk7
glyph        = circle
glyph_size = 4
</rule>

<rule>
importance   = 85
condition    = _VALUE_ > 2
stroke_color = jk8
fill_color   = jk8
glyph        = circle
glyph_size = 5.5
</rule>

<rule>
importance   = 90
condition    = _VALUE_ > 2.5
stroke_color = jk9
fill_color   = jk9
glyph        = circle
glyph_size = 7
</rule>

<rule>
importance   = 95
condition    = _VALUE_ > 3
stroke_color = jk10
fill_color   = jk10
glyph        = circle
glyph_size = 8.5
</rule>

<rule>
importance   = 100 
condition    = _VALUE_ > 4
stroke_color = jk11
fill_color   = jk11
glyph        = circle
glyph_size = 10
</rule>

</rules>

</plot>

############################################################
## Text Plot ##

<plot>

type             = text
color            = black
file             = my_data_files/mutations.txt

# on tick scale
r0 = 1r
r1 = 1r+200p

show_links     = yes
link_dims      = 0p,0p,70p,0p,10p
link_thickness = 2p
link_color     = red
label_size   = 24p
label_font   = condensed

padding  = 0p
rpadding = 0p

label_snuggle         = yes
max_snuggle_distance  = 1r
snuggle_tolerance     = 0.25r
snuggle_sampling      = 2
snuggle_link_overlap_test = yes
snuggle_link_overlap_tolerance = 2p
snuggle_refine        = yes
label_rotate = yes

</plot>

</plots>

############################################################
## Link Plot ##

<links>

z      = 0
radius = 0.77r
bezier_radius = 0.2r

<link segdup>
show         = yes
color        = blue
thickness    = 4
file         = my_data_files/links.txt
record_limit = 1000
</link>

</links>

############################################################
## Run Options
############################################################

anglestep       = 0.5
minslicestep    = 10
beziersamples   = 40
debug           = no
warnings        = no
imagemap        = no

############################################################
## Don't Touch the Following Lines!!!
############################################################
units_ok        = bupr
units_nounit    = n

2) Place the following example data files in "my_data_files"

heatmap.txt

Code:

hs1	0	40000000	0
hs1	40000001	48000000	-2
hs1	48000001	55000000	-4
hs1	55000001	95000000	-2
hs1	95000001	127000000	0
hs1	127000001	247249719	2
hs2	0	242951149	0
hs3	0	199501827	1
hs4	0	191273063	0
hs5	0	180857866	1
hs6	0	106000000	0
hs6	106000001	170899992	-1
hs7	0	158821424	0
hs8	0	128800000	0
hs8	128800001	146274826	1
hs9	0	140273252	3
hs10	0	135374737	0
hs11	0	134452384	0
hs12	0	132349534	0
hs13	0	114142980	-2
hs14	0	106368585	0
hs15	0	100338915	3
hs16	0	41000000	0
hs16	41000001	88827254	-1
hs17	0	5000000	0
hs17	5000001	16000000	-2
hs17	16000001	78774742	0
hs18	0	76117153	0
hs19	0	63811651	1
hs20	0	62435964	0
hs21	0	46944323	1
hs22	0	49691432	0
hsX	0	154913754	-1
hsY	0	57772954	4

scatter.txt

Code:

hs1	0	2300000	0
hs1	2300000	5300000	0.8
hs1	5300000	7100000	1.4
hs1	7100000	9200000	2.9
hs1	9200000	12600000	3.6
hs1	12600000	16100000	4.1
hs1	16100000	20300000	4.8
hs1	20300000	23800000	-0.4
hs1	23800000	27800000	-1.5
hs1	27800000	30000000	-2.1
hs1	30000000	32200000	-2.4
hs1	32200000	34400000	-3.3
hs1	34400000	39600000	-4.9
hs1	39600000	43900000	0.1
hs1	43900000	46500000	0.2
hs1	46500000	51300000	-0.3
hs1	51300000	56200000	0
hs1	56200000	58700000	0.8
hs1	58700000	60900000	1.4
hs1	60900000	68700000	2.9
hs1	68700000	69500000	3.6
hs1	69500000	84700000	4.1
hs1	84700000	88100000	4.8
hs1	88100000	92000000	-0.4
hs1	92000000	94500000	-1.5
hs1	94500000	99400000	-2.1
hs1	99400000	102000000	-2.4
hs1	102000000	107000000	-3.3
hs1	107000000	111600000	-4.9
hs1	111600000	115900000	0.1
hs1	115900000	117600000	0.2
hs1	117600000	120700000	-0.3
hs1	120700000	121100000	0
hs1	121100000	124300000	0.8
hs1	124300000	128000000	1.4
hs1	128000000	142400000	2.9
hs1	142400000	148000000	3.6
hs1	148000000	149600000	4.1
hs1	149600000	153300000	4.8
hs1	153300000	154800000	-0.4
hs1	154800000	157300000	-1.5
hs1	157300000	158800000	-2.1
hs1	158800000	163800000	-2.4
hs1	163800000	165500000	-3.3
hs1	165500000	169100000	-4.9
hs1	169100000	171200000	0.1
hs1	171200000	174300000	0.2
hs1	174300000	178600000	-0.3
hs1	178600000	184000000	0
hs1	184000000	189000000	0.8
hs1	189000000	192100000	1.4
hs1	192100000	197500000	2.9
hs1	197500000	205300000	3.6
hs1	205300000	209500000	4.1
hs1	209500000	212100000	4.8
hs1	212100000	222100000	-0.4
hs1	222100000	222700000	-1.5
hs1	222700000	225100000	-2.1
hs1	225100000	228800000	-2.4
hs1	228800000	232700000	-3.3
hs1	232700000	234600000	-4.9
hs1	234600000	241700000	0.1
hs1	241700000	247249719	0.2
hs2	0	4300000	-0.3
hs2	4300000	7000000	0
hs2	7000000	12800000	0.8
hs2	12800000	17000000	1.4
hs2	17000000	19100000	2.9
hs2	19100000	23900000	3.6
hs2	23900000	27700000	4.1
hs2	27700000	29800000	4.8
hs2	29800000	31900000	-0.4
hs2	31900000	36400000	-1.5
hs2	36400000	38400000	-2.1
hs2	38400000	41600000	-2.4
hs2	41600000	47600000	-3.3
hs2	47600000	52700000	-4.9
hs2	52700000	54800000	0.1
hs2	54800000	61100000	0.2
hs2	61100000	64000000	-0.3
hs2	64000000	70500000	0
hs2	70500000	72600000	0.8
hs2	72600000	73900000	1.4
hs2	73900000	75400000	2.9
hs2	75400000	83700000	3.6
hs2	83700000	91000000	4.1
hs2	91000000	93300000	4.8
hs2	93300000	95700000	-0.4
hs2	95700000	102100000	-1.5
hs2	102100000	105300000	-2.1
hs2	105300000	106700000	-2.4
hs2	106700000	108600000	-3.3
hs2	108600000	113800000	-4.9
hs2	113800000	118600000	0.1
hs2	118600000	122100000	0.2
hs2	122100000	129600000	-0.3
hs2	129600000	132200000	0
hs2	132200000	134800000	0.8
hs2	134800000	136600000	1.4
hs2	136600000	142400000	2.9
hs2	142400000	144700000	3.6
hs2	144700000	148400000	4.1
hs2	148400000	149600000	4.8
hs2	149600000	150300000	-0.4
hs2	150300000	154600000	-1.5
hs2	154600000	159600000	-2.1
hs2	159600000	163500000	-2.4
hs2	163500000	169500000	-3.3
hs2	169500000	177700000	-4.9
hs2	177700000	180400000	0.1
hs2	180400000	182700000	0.2
hs2	182700000	189100000	-0.3
hs2	189100000	191600000	0
hs2	191600000	197100000	0.8
hs2	197100000	203500000	1.4
hs2	203500000	205600000	2.9
hs2	205600000	209100000	3.6
hs2	209100000	215100000	4.1
hs2	215100000	221300000	4.8
hs2	221300000	224900000	-0.4
hs2	224900000	225800000	-1.5
hs2	225800000	230700000	-2.1
hs2	230700000	235300000	-2.4
hs2	235300000	237000000	-3.3
hs2	237000000	242951149	-4.9
hs3	0	3500000	0.1
hs3	3500000	5500000	0.2
hs3	5500000	8700000	-0.3
hs3	8700000	11500000	0
hs3	11500000	12400000	0.8
hs3	12400000	14700000	1.4
hs3	14700000	23800000	2.9
hs3	23800000	26400000	3.6
hs3	26400000	30800000	4.1
hs3	30800000	32100000	4.8
hs3	32100000	36500000	-0.4
hs3	36500000	39300000	-1.5
hs3	39300000	43600000	-2.1
hs3	43600000	44400000	-2.4
hs3	44400000	44700000	-3.3
hs3	44700000	51400000	-4.9
hs3	51400000	51700000	0.1
hs3	51700000	54400000	0.2
hs3	54400000	58500000	-0.3
hs3	58500000	63700000	0
hs3	63700000	71800000	0.8
hs3	71800000	74200000	1.4
hs3	74200000	81800000	2.9
hs3	81800000	83700000	3.6
hs3	83700000	87200000	4.1
hs3	87200000	89400000	4.8
hs3	89400000	91700000	-0.4
hs3	91700000	93200000	-1.5
hs3	93200000	99800000	-2.1
hs3	99800000	101500000	-2.4
hs3	101500000	102500000	-3.3
hs3	102500000	104400000	-4.9
hs3	104400000	107800000	0.1
hs3	107800000	109500000	0.2
hs3	109500000	112800000	-0.3
hs3	112800000	115000000	0
hs3	115000000	118800000	0.8
hs3	118800000	120500000	1.4
hs3	120500000	123400000	2.9
hs3	123400000	125400000	3.6
hs3	125400000	127700000	4.1
hs3	127700000	131500000	4.8
hs3	131500000	135700000	-0.4
hs3	135700000	137400000	-1.5
hs3	137400000	140400000	-2.1
hs3	140400000	144400000	-2.4
hs3	144400000	150400000	-3.3
hs3	150400000	153500000	-4.9
hs3	153500000	156300000	0.1
hs3	156300000	158100000	0.2
hs3	158100000	159900000	-0.3
hs3	159900000	161200000	0
hs3	161200000	169200000	0.8
hs3	169200000	172500000	1.4
hs3	172500000	177300000	2.9
hs3	177300000	180600000	3.6
hs3	180600000	184200000	4.1
hs3	184200000	186000000	4.8
hs3	186000000	187500000	-0.4
hs3	187500000	189400000	-1.5
hs3	189400000	193800000	-2.1
hs3	193800000	199501827	-2.4
hs4	0	3100000	-3.3
hs4	3100000	5200000	-4.9
hs4	5200000	10900000	0.1
hs4	10900000	15300000	0.2
hs4	15300000	18500000	-0.3
hs4	18500000	23100000	0
hs4	23100000	27900000	0.8
hs4	27900000	35500000	1.4
hs4	35500000	40900000	2.9
hs4	40900000	45600000	3.6
hs4	45600000	48700000	4.1
hs4	48700000	50700000	4.8
hs4	50700000	52400000	-0.4
hs4	52400000	59200000	-1.5
hs4	59200000	66300000	-2.1
hs4	66300000	70400000	-2.4
hs4	70400000	76500000	-3.3
hs4	76500000	79200000	-4.9
hs4	79200000	82600000	0.1
hs4	82600000	84300000	0.2
hs4	84300000	87100000	-0.3
hs4	87100000	88200000	0
hs4	88200000	94000000	0.8
hs4	94000000	95400000	1.4
hs4	95400000	99100000	2.9
hs4	99100000	102500000	3.6
hs4	102500000	107900000	4.1
hs4	107900000	114100000	4.8
hs4	114100000	120600000	-0.4
hs4	120600000	124000000	-1.5
hs4	124000000	129100000	-2.1
hs4	129100000	131300000	-2.4
hs4	131300000	139500000	-3.3
hs4	139500000	141700000	-4.9
hs4	141700000	145000000	0.1
hs4	145000000	147700000	0.2
hs4	147700000	151000000	-0.3
hs4	151000000	155100000	0
hs4	155100000	161500000	0.8
hs4	161500000	164500000	1.4
hs4	164500000	170400000	2.9
hs4	170400000	172200000	3.6
hs4	172200000	176600000	4.1
hs4	176600000	177800000	4.8
hs4	177800000	182600000	-0.4
hs4	182600000	187300000	-1.5
hs4	187300000	191273063	-2.1
hs5	0	4400000	-2.4
hs5	4400000	6000000	-3.3
hs5	6000000	8200000	-4.9
hs5	8200000	15100000	0.1
hs5	15100000	18500000	0.2
hs5	18500000	23300000	-0.3
hs5	23300000	24700000	0
hs5	24700000	29300000	0.8
hs5	29300000	34400000	1.4
hs5	34400000	38500000	2.9
hs5	38500000	42400000	3.6
hs5	42400000	45800000	4.1
hs5	45800000	47700000	4.8
hs5	47700000	50500000	-0.4
hs5	50500000	58900000	-1.5
hs5	58900000	63000000	-2.1
hs5	63000000	63700000	-2.4
hs5	63700000	66500000	-3.3
hs5	66500000	68400000	-4.9
hs5	68400000	73300000	0.1
hs5	73300000	76400000	0.2
hs5	76400000	81300000	-0.3
hs5	81300000	82800000	0
hs5	82800000	91900000	0.8
hs5	91900000	97300000	1.4
hs5	97300000	102800000	2.9
hs5	102800000	104500000	3.6
hs5	104500000	109600000	4.1
hs5	109600000	111500000	4.8
hs5	111500000	113100000	-0.4
hs5	113100000	115200000	-1.5
hs5	115200000	121500000	-2.1
hs5	121500000	127300000	-2.4
hs5	127300000	130400000	-3.3
hs5	130400000	135400000	-4.9
hs5	135400000	139000000	0.1
hs5	139000000	143100000	0.2
hs5	143100000	147200000	-0.3
hs5	147200000	152100000	0
hs5	152100000	155600000	0.8
hs5	155600000	159900000	1.4
hs5	159900000	167400000	2.9
hs5	167400000	172200000	3.6
hs5	172200000	176500000	4.1
hs5	176500000	180857866	4.8
hs6	0	2300000	-0.4
hs6	2300000	4100000	-1.5
hs6	4100000	7000000	-2.1
hs6	7000000	10600000	-2.4
hs6	10600000	11200000	-3.3
hs6	11200000	13500000	-4.9
hs6	13500000	15500000	0.1
hs6	15500000	23500000	0.2
hs6	23500000	26100000	-0.3
hs6	26100000	29900000	0
hs6	29900000	31900000	0.8
hs6	31900000	33600000	1.4
hs6	33600000	36800000	2.9
hs6	36800000	40600000	3.6
hs6	40600000	45200000	4.1
hs6	45200000	51100000	4.8
hs6	51100000	52600000	-0.4
hs6	52600000	57200000	-1.5
hs6	57200000	58400000	-2.1
hs6	58400000	60500000	-2.4
hs6	60500000	63400000	-3.3
hs6	63400000	63500000	-4.9
hs6	63500000	70000000	0.1
hs6	70000000	75900000	0.2
hs6	75900000	83900000	-0.3
hs6	83900000	84700000	0
hs6	84700000	87500000	0.8
hs6	87500000	92100000	1.4
hs6	92100000	98700000	2.9
hs6	98700000	99900000	3.6
hs6	99900000	104800000	4.1
hs6	104800000	113900000	4.8
hs6	113900000	117100000	-0.4
hs6	117100000	118600000	-1.5
hs6	118600000	126200000	-2.1
hs6	126200000	127300000	-2.4
hs6	127300000	130400000	-3.3
hs6	130400000	131300000	-4.9
hs6	131300000	135200000	0.1
hs6	135200000	139100000	0.2
hs6	139100000	142900000	-0.3
hs6	142900000	145700000	0
hs6	145700000	149100000	0.8
hs6	149100000	152600000	1.4
hs6	152600000	155600000	2.9
hs6	155600000	160900000	3.6
hs6	160900000	164400000	4.1
hs6	164400000	170899992	4.8
hs7	0	2100000	-0.4
hs7	2100000	4500000	-1.5
hs7	4500000	7200000	-2.1
hs7	7200000	13300000	-2.4
hs7	13300000	15200000	-3.3
hs7	15200000	19500000	-4.9
hs7	19500000	24900000	0.1
hs7	24900000	28000000	0.2
hs7	28000000	31800000	-0.3
hs7	31800000	35600000	0
hs7	35600000	37500000	0.8
hs7	37500000	43300000	1.4
hs7	43300000	46600000	2.9
hs7	46600000	49800000	3.6
hs7	49800000	50900000	4.1
hs7	50900000	53900000	4.8
hs7	53900000	57400000	-0.4
hs7	57400000	59100000	-1.5
hs7	59100000	61100000	-2.1
hs7	61100000	66100000	-2.4
hs7	66100000	71800000	-3.3
hs7	71800000	77400000	-4.9
hs7	77400000	86200000	0.1
hs7	86200000	88000000	0.2
hs7	88000000	90900000	-0.3
hs7	90900000	92600000	0
hs7	92600000	97900000	0.8
hs7	97900000	104400000	1.4
hs7	104400000	105900000	2.9
hs7	105900000	107200000	3.6
hs7	107200000	114400000	4.1
hs7	114400000	117200000	4.8
hs7	117200000	120900000	-0.4
hs7	120900000	123600000	-1.5
hs7	123600000	126900000	-2.1
hs7	126900000	129000000	-2.4
hs7	129000000	130100000	-3.3
hs7	130100000	132400000	-4.9
hs7	132400000	137300000	0.1
hs7	137300000	142800000	0.2
hs7	142800000	147500000	-0.3
hs7	147500000	152200000	0
hs7	152200000	154700000	0.8
hs7	154700000	158821424	1.4
hs8	0	2200000	2.9
hs8	2200000	6200000	3.6
hs8	6200000	12700000	4.1
hs8	12700000	19100000	4.8
hs8	19100000	23400000	-0.4
hs8	23400000	27400000	-1.5
hs8	27400000	29700000	-2.1
hs8	29700000	38500000	-2.4
hs8	38500000	39500000	-3.3
hs8	39500000	39900000	-4.9
hs8	39900000	43200000	0.1
hs8	43200000	45200000	0.2
hs8	45200000	48100000	-0.3
hs8	48100000	50400000	0
hs8	50400000	52800000	0.8
hs8	52800000	55600000	1.4
hs8	55600000	61700000	2.9
hs8	61700000	62400000	3.6
hs8	62400000	66100000	4.1
hs8	66100000	68100000	4.8
hs8	68100000	70600000	-0.4
hs8	70600000	74000000	-1.5
hs8	74000000	78500000	-2.1
hs8	78500000	80300000	-2.4
hs8	80300000	84900000	-3.3
hs8	84900000	87200000	-4.9
hs8	87200000	93500000	0.1
hs8	93500000	99100000	0.2
hs8	99100000	101600000	-0.3
hs8	101600000	106100000	0
hs8	106100000	110600000	0.8
hs8	110600000	112200000	1.4
hs8	112200000	117700000	2.9
hs8	117700000	119200000	3.6
hs8	119200000	122500000	4.1
hs8	122500000	127300000	4.8
hs8	127300000	131500000	-0.4
hs8	131500000	136500000	-1.5
hs8	136500000	140000000	-2.1
hs8	140000000	146274826	-2.4
hs9	0	2200000	-3.3
hs9	2200000	4600000	-4.9
hs9	4600000	9000000	0.1
hs9	9000000	14100000	0.2
hs9	14100000	16600000	-0.3
hs9	16600000	18500000	0
hs9	18500000	19900000	0.8
hs9	19900000	25500000	1.4
hs9	25500000	28100000	2.9
hs9	28100000	32800000	3.6
hs9	32800000	36300000	4.1
hs9	36300000	38000000	4.8
hs9	38000000	40200000	-0.4
hs9	40200000	42400000	-1.5
hs9	42400000	46700000	-2.1
hs9	46700000	51800000	-2.4
hs9	51800000	60300000	-3.3
hs9	60300000	70000000	-4.9
hs9	70000000	70500000	0.1
hs9	70500000	72700000	0.2
hs9	72700000	73100000	-0.3
hs9	73100000	79300000	0
hs9	79300000	80300000	0.8
hs9	80300000	83400000	1.4
hs9	83400000	86100000	2.9
hs9	86100000	89600000	3.6
hs9	89600000	91000000	4.1
hs9	91000000	93000000	4.8
hs9	93000000	95600000	-0.4
hs9	95600000	98200000	-1.5
hs9	98200000	101600000	-2.1
hs9	101600000	107200000	-2.4
hs9	107200000	110300000	-3.3
hs9	110300000	113900000	-4.9
hs9	113900000	116700000	0.1
hs9	116700000	122000000	0.2
hs9	122000000	125800000	-0.3
hs9	125800000	129300000	0
hs9	129300000	132500000	0.8
hs9	132500000	132800000	1.4
hs9	132800000	134900000	2.9
hs9	134900000	136600000	3.6
hs9	136600000	140273252	4.1
hsX	0	4300000	4.8
hsX	4300000	6000000	-0.4
hsX	6000000	9500000	-1.5
hsX	9500000	17100000	-2.1
hsX	17100000	19200000	-2.4
hsX	19200000	21800000	-3.3
hsX	21800000	24900000	-4.9
hsX	24900000	29400000	0.1
hsX	29400000	31500000	0.2
hsX	31500000	37500000	-0.3
hsX	37500000	42300000	0
hsX	42300000	47300000	0.8
hsX	47300000	49700000	1.4
hsX	49700000	54700000	2.9
hsX	54700000	56600000	3.6
hsX	56600000	59500000	4.1
hsX	59500000	65000000	4.8
hsX	65000000	65100000	-0.4
hsX	65100000	67700000	-1.5
hsX	67700000	72200000	-2.1
hsX	72200000	73800000	-2.4
hsX	73800000	76000000	-3.3
hsX	76000000	84500000	-4.9
hsX	84500000	86200000	0.1
hsX	86200000	91900000	0.2
hsX	91900000	93500000	-0.3
hsX	93500000	98200000	0
hsX	98200000	102500000	0.8
hsX	102500000	103600000	1.4
hsX	103600000	110500000	2.9
hsX	110500000	116800000	3.6
hsX	116800000	120700000	4.1
hsX	120700000	129800000	4.8
hsX	129800000	130300000	-0.4
hsX	130300000	133500000	-1.5
hsX	133500000	137800000	-2.1
hsX	137800000	140100000	-2.4
hsX	140100000	141900000	-3.3
hsX	141900000	146900000	-4.9
hsX	146900000	154913754	0.1
hsY	0	1700000	0.2
hsY	1700000	3300000	-0.3
hsY	3300000	11200000	0
hsY	11200000	11300000	0.8
hsY	11300000	12500000	1.4
hsY	12500000	14300000	2.9
hsY	14300000	19000000	3.6
hsY	19000000	21300000	4.1
hsY	21300000	25400000	4.8
hsY	25400000	27200000	-0.4
hsY	27200000	57772954	-1.5
hs10	0	3000000	-2.1
hs10	3000000	3800000	-2.4
hs10	3800000	6700000	-3.3
hs10	6700000	12300000	-4.9
hs10	12300000	17300000	0.1
hs10	17300000	19900000	0.2
hs10	19900000	20500000	-0.3
hs10	20500000	22800000	0
hs10	22800000	24100000	0.8
hs10	24100000	28300000	1.4
hs10	28300000	31400000	2.9
hs10	31400000	34500000	3.6
hs10	34500000	38800000	4.1
hs10	38800000	40300000	4.8
hs10	40300000	42100000	-0.4
hs10	42100000	46100000	-1.5
hs10	46100000	50100000	-2.1
hs10	50100000	53300000	-2.4
hs10	53300000	61200000	-3.3
hs10	61200000	64800000	-4.9
hs10	64800000	71300000	0.1
hs10	71300000	74600000	0.2
hs10	74600000	77400000	-0.3
hs10	77400000	82000000	0
hs10	82000000	87900000	0.8
hs10	87900000	89600000	1.4
hs10	89600000	92900000	2.9
hs10	92900000	94200000	3.6
hs10	94200000	98000000	4.1
hs10	98000000	99400000	4.8
hs10	99400000	102000000	-0.4
hs10	102000000	103000000	-1.5
hs10	103000000	104900000	-2.1
hs10	104900000	105700000	-2.4
hs10	105700000	111800000	-3.3
hs10	111800000	114900000	-4.9
hs10	114900000	119100000	0.1
hs10	119100000	121700000	0.2
hs10	121700000	123100000	-0.3
hs10	123100000	127400000	0
hs10	127400000	130500000	0.8
hs10	130500000	135374737	1.4
hs11	0	2800000	2.9
hs11	2800000	10700000	3.6
hs11	10700000	12600000	4.1
hs11	12600000	16100000	4.8
hs11	16100000	21600000	-0.4
hs11	21600000	26000000	-1.5
hs11	26000000	27200000	-2.1
hs11	27200000	31000000	-2.4
hs11	31000000	36400000	-3.3
hs11	36400000	43400000	-4.9
hs11	43400000	48800000	0.1
hs11	48800000	51400000	0.2
hs11	51400000	52900000	-0.3
hs11	52900000	56400000	0
hs11	56400000	59700000	0.8
hs11	59700000	61400000	1.4
hs11	61400000	63100000	2.9
hs11	63100000	67100000	3.6
hs11	67100000	69200000	4.1
hs11	69200000	70700000	4.8
hs11	70700000	74900000	-0.4
hs11	74900000	76700000	-1.5
hs11	76700000	85300000	-2.1
hs11	85300000	87900000	-2.4
hs11	87900000	92300000	-3.3
hs11	92300000	96700000	-4.9
hs11	96700000	101600000	0.1
hs11	101600000	102400000	0.2
hs11	102400000	110000000	-0.3
hs11	110000000	112800000	0
hs11	112800000	115400000	0.8
hs11	115400000	120700000	1.4
hs11	120700000	123500000	2.9
hs11	123500000	127400000	3.6
hs11	127400000	130300000	4.1
hs11	130300000	134452384	4.8
hs12	0	3100000	-0.4
hs12	3100000	5300000	-1.5
hs12	5300000	10000000	-2.1
hs12	10000000	12600000	-2.4
hs12	12600000	14800000	-3.3
hs12	14800000	19900000	-4.9
hs12	19900000	21200000	0.1
hs12	21200000	26300000	0.2
hs12	26300000	27700000	-0.3
hs12	27700000	30600000	0
hs12	30600000	33200000	0.8
hs12	33200000	35400000	1.4
hs12	35400000	36500000	2.9
hs12	36500000	44600000	3.6
hs12	44600000	47400000	4.1
hs12	47400000	48400000	4.8
hs12	48400000	53100000	-0.4
hs12	53100000	55200000	-1.5
hs12	55200000	56300000	-2.1
hs12	56300000	61400000	-2.4
hs12	61400000	63400000	-3.3
hs12	63400000	66000000	-4.9
hs12	66000000	69800000	0.1
hs12	69800000	74100000	0.2
hs12	74100000	78700000	-0.3
hs12	78700000	85100000	0
hs12	85100000	87500000	0.8
hs12	87500000	91200000	1.4
hs12	91200000	94800000	2.9
hs12	94800000	100000000	3.6
hs12	100000000	102400000	4.1
hs12	102400000	107500000	4.8
hs12	107500000	110200000	-0.4
hs12	110200000	110800000	-1.5
hs12	110800000	112800000	-2.1
hs12	112800000	115300000	-2.4
hs12	115300000	116700000	-3.3
hs12	116700000	119100000	-4.9
hs12	119100000	124500000	0.1
hs12	124500000	128700000	0.2
hs12	128700000	132349534	-0.3
hs13	0	3800000	0
hs13	3800000	8300000	0.8
hs13	8300000	13500000	1.4
hs13	13500000	16000000	2.9
hs13	16000000	18400000	3.6
hs13	18400000	22200000	4.1
hs13	22200000	24400000	4.8
hs13	24400000	26700000	-0.4
hs13	26700000	27800000	-1.5
hs13	27800000	31100000	-2.1
hs13	31100000	32900000	-2.4
hs13	32900000	34700000	-3.3
hs13	34700000	39500000	-4.9
hs13	39500000	44300000	0.1
hs13	44300000	45900000	0.2
hs13	45900000	46200000	-0.3
hs13	46200000	48900000	0
hs13	48900000	52200000	0.8
hs13	52200000	57600000	1.4
hs13	57600000	60500000	2.9
hs13	60500000	64100000	3.6
hs13	64100000	67200000	4.1
hs13	67200000	72100000	4.8
hs13	72100000	74200000	-0.4
hs13	74200000	76000000	-1.5
hs13	76000000	77800000	-2.1
hs13	77800000	86500000	-2.4
hs13	86500000	88800000	-3.3
hs13	88800000	93800000	-4.9
hs13	93800000	97000000	0.1
hs13	97000000	98100000	0.2
hs13	98100000	100500000	-0.3
hs13	100500000	103700000	0
hs13	103700000	105800000	0.8
hs13	105800000	109100000	1.4
hs13	109100000	114142980	2.9
hs14	0	3100000	3.6
hs14	3100000	6700000	4.1
hs14	6700000	13600000	4.8
hs14	13600000	15600000	-0.4
hs14	15600000	19100000	-1.5
hs14	19100000	23600000	-2.1
hs14	23600000	31800000	-2.4
hs14	31800000	34100000	-3.3
hs14	34100000	35600000	-4.9
hs14	35600000	36900000	0.1
hs14	36900000	41000000	0.2
hs14	41000000	43200000	-0.3
hs14	43200000	48300000	0
hs14	48300000	52300000	0.8
hs14	52300000	54400000	1.4
hs14	54400000	55800000	2.9
hs14	55800000	61200000	3.6
hs14	61200000	64000000	4.1
hs14	64000000	67000000	4.8
hs14	67000000	69300000	-0.4
hs14	69300000	72900000	-1.5
hs14	72900000	78400000	-2.1
hs14	78400000	82600000	-2.4
hs14	82600000	84000000	-3.3
hs14	84000000	88900000	-4.9
hs14	88900000	90500000	0.1
hs14	90500000	92800000	0.2
hs14	92800000	95400000	-0.3
hs14	95400000	100400000	0
hs14	100400000	102200000	0.8
hs14	102200000	103000000	1.4
hs14	103000000	106368585	2.9
hs15	0	3500000	3.6
hs15	3500000	7900000	4.1
hs15	7900000	14100000	4.8
hs15	14100000	17000000	-0.4
hs15	17000000	18400000	-1.5
hs15	18400000	23300000	-2.1
hs15	23300000	25700000	-2.4
hs15	25700000	28000000	-3.3
hs15	28000000	29000000	-4.9
hs15	29000000	31400000	0.1
hs15	31400000	37900000	0.2
hs15	37900000	40700000	-0.3
hs15	40700000	41400000	0
hs15	41400000	42700000	0.8
hs15	42700000	47600000	1.4
hs15	47600000	51100000	2.9
hs15	51100000	55800000	3.6
hs15	55800000	57100000	4.1
hs15	57100000	61500000	4.8
hs15	61500000	64900000	-0.4
hs15	64900000	65000000	-1.5
hs15	65000000	65300000	-2.1
hs15	65300000	70400000	-2.4
hs15	70400000	73100000	-3.3
hs15	73100000	74400000	-4.9
hs15	74400000	76100000	0.1
hs15	76100000	79500000	0.2
hs15	79500000	83000000	-0.3
hs15	83000000	86900000	0
hs15	86900000	92100000	0.8
hs15	92100000	96300000	1.4
hs15	96300000	100338915	2.9
hs16	0	6300000	3.6
hs16	6300000	10300000	4.1
hs16	10300000	12500000	4.8
hs16	12500000	14700000	-0.4
hs16	14700000	16700000	-1.5
hs16	16700000	20500000	-2.1
hs16	20500000	21700000	-2.4
hs16	21700000	27600000	-3.3
hs16	27600000	34400000	-4.9
hs16	34400000	38200000	0.1
hs16	38200000	40700000	0.2
hs16	40700000	45500000	-0.3
hs16	45500000	51200000	0
hs16	51200000	54500000	0.8
hs16	54500000	56700000	1.4
hs16	56700000	65200000	2.9
hs16	65200000	69400000	3.6
hs16	69400000	69800000	4.1
hs16	69800000	73300000	4.8
hs16	73300000	78200000	-0.4
hs16	78200000	80500000	-1.5
hs16	80500000	82700000	-2.1
hs16	82700000	85600000	-2.4
hs16	85600000	87200000	-3.3
hs16	87200000	88827254	-4.9
hs17	0	3600000	0.1
hs17	3600000	6800000	0.2
hs17	6800000	11200000	-0.3
hs17	11200000	15900000	0
hs17	15900000	22100000	0.8
hs17	22100000	22200000	1.4
hs17	22200000	23200000	2.9
hs17	23200000	28800000	3.6
hs17	28800000	35400000	4.1
hs17	35400000	35600000	4.8
hs17	35600000	37800000	-0.4
hs17	37800000	41900000	-1.5
hs17	41900000	44800000	-2.1
hs17	44800000	47600000	-2.4
hs17	47600000	54900000	-3.3
hs17	54900000	55600000	-4.9
hs17	55600000	58400000	0.1
hs17	58400000	59900000	0.2
hs17	59900000	61600000	-0.3
hs17	61600000	64600000	0
hs17	64600000	68400000	0.8
hs17	68400000	72200000	1.4
hs17	72200000	72900000	2.9
hs17	72900000	78774742	3.6
hs18	0	2900000	4.1
hs18	2900000	7200000	4.8
hs18	7200000	8500000	-0.4
hs18	8500000	10900000	-1.5
hs18	10900000	15400000	-2.1
hs18	15400000	16100000	-2.4
hs18	16100000	17300000	-3.3
hs18	17300000	23300000	-4.9
hs18	23300000	31000000	0.1
hs18	31000000	35500000	0.2
hs18	35500000	41800000	-0.3
hs18	41800000	46400000	0
hs18	46400000	52000000	0.8
hs18	52000000	54400000	1.4
hs18	54400000	57100000	2.9
hs18	57100000	59800000	3.6
hs18	59800000	64900000	4.1
hs18	64900000	66900000	4.8
hs18	66900000	71300000	-0.4
hs18	71300000	76117153	-1.5
hs19	0	6900000	-2.1
hs19	6900000	12600000	-2.4
hs19	12600000	13800000	-3.3
hs19	13800000	16100000	-4.9
hs19	16100000	19800000	0.1
hs19	19800000	26700000	0.2
hs19	26700000	28500000	-0.3
hs19	28500000	30200000	0
hs19	30200000	37100000	0.8
hs19	37100000	40300000	1.4
hs19	40300000	43000000	2.9
hs19	43000000	43400000	3.6
hs19	43400000	47800000	4.1
hs19	47800000	50000000	4.8
hs19	50000000	53800000	-0.4
hs19	53800000	57600000	-1.5
hs19	57600000	59100000	-2.1
hs19	59100000	61400000	-2.4
hs19	61400000	63811651	-3.3
hs20	0	5000000	-4.9
hs20	5000000	9000000	0.1
hs20	9000000	11900000	0.2
hs20	11900000	17800000	-0.3
hs20	17800000	21200000	0
hs20	21200000	22300000	0.8
hs20	22300000	25700000	1.4
hs20	25700000	27100000	2.9
hs20	27100000	28400000	3.6
hs20	28400000	31500000	4.1
hs20	31500000	33900000	4.8
hs20	33900000	37100000	-0.4
hs20	37100000	41100000	-1.5
hs20	41100000	41600000	-2.1
hs20	41600000	45800000	-2.4
hs20	45800000	49200000	-3.3
hs20	49200000	54400000	-4.9
hs20	54400000	55900000	0.1
hs20	55900000	57900000	0.2
hs20	57900000	62435964	-0.3
hs21	0	2900000	0
hs21	2900000	6300000	0.8
hs21	6300000	10000000	1.4
hs21	10000000	12300000	2.9
hs21	12300000	13200000	3.6
hs21	13200000	15300000	4.1
hs21	15300000	22900000	4.8
hs21	22900000	25800000	-0.4
hs21	25800000	30500000	-1.5
hs21	30500000	34700000	-2.1
hs21	34700000	36700000	-2.4
hs21	36700000	38600000	-3.3
hs21	38600000	41400000	-4.9
hs21	41400000	46944323	0.1
hs22	0	3000000	0.2
hs22	3000000	6600000	-0.3
hs22	6600000	9600000	0
hs22	9600000	11800000	0.8
hs22	11800000	16300000	1.4
hs22	16300000	20500000	2.9
hs22	20500000	21800000	3.6
hs22	21800000	24300000	4.1
hs22	24300000	27900000	4.8
hs22	27900000	30500000	-0.4
hs22	30500000	35900000	-1.5
hs22	35900000	39300000	-2.1
hs22	39300000	42600000	-2.4
hs22	42600000	47000000	-3.3
hs22	47000000	48200000	-4.9
hs22	48200000	49691432	0.1

mutations.txt

Code:

hs1	71600000	71600010	NEGR1	
hs2	25280000	25280010	KRAS	
hs5	162890000	162890010	HMMR	color=red,link_color=red
hs6	138230000	138230010	TNFAIP3	color=red,link_color=blue
hs8	38250000	38250010	WHSC1L1	
hs13	47832000	47832010	RB1	color=black,link_color=blue
hs14	102320000	102320010	TRAF3	color=black,link_color=blue
hs14	102328000	102328010	TRAF3	color=red,link_color=red
hs17	7530000	7530010	TP53	color=red,link_color=blue
hsX	44790000	44790010	KDM6A	color=red,link_color=blue

links.txt

Code:

intra1	hs1	40000000	40000010	color=green
intra1	hs1	55000001	55000011	color=green
intra2	hs1	48000000	48000010	color=green
intra2	hs1	95000001	95000011	color=green
intra3	hs1	127000001	127000011	color=green
intra3	hs1	247230000	247240000	color=green
tx1	hs6	106000000	106000010	color=red
tx1	hs8	128800000	128800010	color=red
tx2	hs11	69160000	69160010	
tx2	hs14	103000000	103000010	
intra4	hs17	5000000	5000010	color=green
intra4	hs17	16000001	16000011	color=green

3) Run the example test

Code:

cd ngs/applications/circos-0.52

circos -conf my_config_files/myeloma_circos.conf

Figure Legend:
Mutated genes are marked on the outside of the ideogram. Line and font colors are used to represent different zygosity and type of mutation. Inner heatmap is copy number data. Inner scatter plot is gene expression values. Inner line links represent inter and intra chromosomal rearrangements with balanced and unbalanced inter-chromosomal events shown in different colors.

Attached Files

myeloma_example.jpg (67.9 KB, 279 views)

**Novice** · 02-21-2011, 06:59 AM

Originally posted by honey View Post

Novice,
I have used the beta version of Avadis and will be willing to know how it work. However I have not found toll as user friendly as Gene Spring. The level of customer support has alos declined...

Honey,

I do agree with you, Avadis is not as user friendly as the Gene Spring, but it worked much better for me than CLCBio. The CLC crashed in my hands 4-5 times (lost the track of how many it was) with the same data ran on Avadis. I'll make a new thread about my evaluation, because I have some questions I need answering, so if you want you can read that.

Cheers,

**Joann** · 02-21-2011, 11:12 AM

A Circos Example

A Circos Example
***A Simple Example from the Multiple Myeloma World***

Would someone kindly post the finished graphic obtained from this example. Many thanks.

**Jon_Keats** · 02-22-2011, 10:07 AM

Originally posted by Joann View Post

A Circos Example
***A Simple Example from the Multiple Myeloma World***

Would someone kindly post the finished graphic obtained from this example. Many thanks.

Sorry I got lazy and forgot I needed to down sample the image so it was small enough to upload. The image is now attached to the example entry.

Best of luck,

Jonathan

**raimo** · 02-23-2011, 02:06 AM

What a great thread...

Dear Jonathan,

thank you so much for sharing all this! This is tremendously helpful for the newbie! Keep up the great work!
Best
Raimo

**Jon_Keats** · 03-07-2011, 10:42 PM

TopHat-Cufflinks Paired End Pipeline

I've been meaning to post this for a while but didn't as it is written for our HPC environment instead of a MAC but as currently modified it should work fine on any Unix environment. I'll try to update it to fit the standard workflow/folder structure I've used in the past. Currently it is designed to require you to update the script for each sample you are running and will pass the data from illumina format fastq files to tophat alignments and cufflinks expression estimates.

The top of the script should be modified to something like

Code:

## MODIFY SCRIPT SETTINGS BELOW FOR EACH RUN

SAMPLE_NAME=MC0005_MCR0728_RNAseq
#Enter sample name less read ID, thus "Sample1_R1.txt" would be "Sample1"
GENOME_REFERENCE=/scratch/jkeats/refgenomes/bowtie_indexed/hg19
#This should be something like "/scratch/jkeats/refgenomes/bowtie_indexed/Genome"
GTF_FILE=/scratch/jkeats/refgenomes/annotation_tracks/GRCh37_E60_BowtieIndexCompatible.gtf
#This should be used if using ref option
#EXCLUSION_FILE=/scratch/jkeats/refgenomes/annotation_tracks/GRCh37_E60_CufflinksExcludedTranscripts.gtf
#This should be used if using an excludion file for cufflinks abundance estimates
GENOME_NAME=hg19
#This is used to rename result files to include the genome version
PROTOCOL_TAG=TophatPE_E60GTF
#This is a tag used to rename the results files with a unique tag
PROTOCOL_TAG2=CufflinksE60GTF_NoMask
#This is a tag used to rename the results files with a unique tag for the cufflinks output files
MATE_INNER_DIST=178
#Mean insert size calculated after BWA alignment to transcriptome reference less read length (mean insert = 400 - (50bp x 2) = 300bp Inner Distance
MATE_INNER_STD=45
#Standard deviation of insert size calculated after BWA alignment to tanscriptome scaled to inner distance (insert STD = 40 x (300bp / 400bp) = 30bp Inner STD
TOPHAT_CORES=8
#This is used to allow multi-threading or parallel processing during the tophat alignment steps
#This number should match the number of nodes/cores requested in the PBS header above
ALIGNMENT_TYPE=NoGaps
#The newest version of Tophat supports small gaps by default 3 if the --allow-indels option is set
#YOU MUST MODIFY LINE XXX TO INCLUDE THE "--allow-indels" option
#You can change the default indel size using "--max-insertion-length <int>" and "--max-deletion-length <int>" if you include this option
SAMTOOLS_VERSION=Samtools_Version0.1.12a
#Get version number my typing "samtools" once logged on to saguaro (DO NOT INCLUDE SUBVERSION IN BRACKETS)
CUFFLINKS_VERSION=Cufflinks_Version0.9.3
#Get version number my typing "cufflinks" once logged on to saguaro

Code:

#!/bin/bash

# Created by Jonathan Keats on 12/30/10.
# Copyright 2010 Translational Genomics Research Institute. All rights reserved.

##########################################################
##########################################################														
## MODIFY SCRIPT SETTINGS BELOW FOR EACH RUN

SAMPLE_NAME=***Enter Sample Name Here***
#Enter sample name less read ID, thus "Sample1_R1.txt" would be "Sample1"
GENOME_REFERENCE=/scratch/jkeats/refgenomes/bowtie_indexed/hg19
#This should be something like "/scratch/jkeats/refgenomes/bowtie_indexed/Genome"
GTF_FILE=/scratch/jkeats/refgenomes/annotation_tracks/GRCh37_E60_BowtieIndexCompatible.gtf
#This should be used if using ref option
#EXCLUSION_FILE=/scratch/jkeats/refgenomes/annotation_tracks/GRCh37_E60_CufflinksExcludedTranscripts.gtf
#This should be used if using an excludion file for cufflinks abundance estimates
GENOME_NAME=hg19
#This is used to rename result files to include the genome version
PROTOCOL_TAG=***This should be "AlignerMethod_Constraints" such as "TophatPE_E60GFF" or "TophatSE_DeNovo"
#This is a tag used to rename the results files with a unique tag
PROTOCOL_TAG2=***This should be "CufflinksE60GTF_NoMask" or "CufflinksDeNovo_Masked"
#This is a tag used to rename the results files with a unique tag for the cufflinks output files
MATE_INNER_DIST=***value bp***
#Mean insert size calculated after BWA alignment to transcriptome reference less read length (mean insert = 400 - (50bp x 2) = 300bp Inner Distance
MATE_INNER_STD=***value bp***
#Standard deviation of insert size calculated after BWA alignment to tanscriptome scaled to inner distance (insert STD = 40 x (300bp / 400bp) = 30bp Inner STD
TOPHAT_CORES=***Enter Number of Cores/Threads***
#This is used to allow multi-threading or parallel processing during the tophat alignment steps
#This number should match the number of nodes/cores requested in the PBS header above
ALIGNMENT_TYPE=*** Either "NoGaps" or "InDel(plus numeric limit) default is InDel3"
#The newest version of Tophat supports small gaps by default 3 if the --allow-indels option is set
#YOU MUST MODIFY LINE XXX TO INCLUDE THE "--allow-indels" option
#You can change the default indel size using "--max-insertion-length <int>" and "--max-deletion-length <int>" if you include this option
SAMTOOLS_VERSION=***Enter version info***
#Get version number my typing "samtools" once logged on to saguaro (no spaces)(DO NOT INCLUDE SUBVERSION IN BRACKETS)
CUFFLINKS_VERSION=***Enter version info***
#Get version number my typing "cufflinks" once logged on to saguaro (no spaces)

##########################################################	
##########################################################
##	Notes: This script script is to be launched from a common folder with the raw data
##	
##	Requirements:	1) Input files must follow "Sample_R1.txt" and "Sample_R2.txt"
##				2) You must load or have the following applications in your path:
##					a) Tophat (v1.2.0 or later to support InDels) 
##					b) Cufflinks
##					c) Samtools
##					d) Java
##						i)   Picard SortSam.jar	
##						ii)  Picard MarkDuplicates.jar
##					        iii) Picard CollectAlignmentSummaryMetrics.jar
##						iv)  Picard MeanQualityByCycle.jar
##					e) R
##########################################################
##########################################################	
## THE FOLLOWING LINES ARE REQUIRED TO RUN THE SCRIPT


PICARD_PATH=$HOME/local/bin
#I still can't figure out how to list "/local/bin" in the java path but this works


##########################################################
##########################################################	
## THE REMAINING LINES OF THIS SCRIPT SHOULD NOT BE MODIFIED
##########################################################
##########################################################

#The following step creates the log file in the current subdirectory

echo ***STARTING ${SAMPLE_NAME} ANALYSIS BATCH*** >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo -------------------------------------------------------- >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log

#The following step prints the version numbers of the programs to the log file
echo >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo The following applications will be used: >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
bowtie --version >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
tophat --version >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo ${SAMTOOLS_VERSION} >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo ${CUFFLINKS_VERSION} >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo -------------------------------------------------------- >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log

# In this first step we will create a custom directory for this sample
# Directory Name = "Sample_Name"

echo >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo ***Creating Pipeline Directory Structure*** >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log

mkdir -p ${SAMPLE_NAME}/bamfile_dupsmarked

echo ***Pipeline Directory Structure Created*** >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo -------------------------------------------------------- >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log

# In the following step we will move the raw data files from the current location to the analysis directory

echo >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo Moving fastq files to analysis directory >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo The following files will be moved: >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo ${SAMPLE_NAME}_R1.txt >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo ${SAMPLE_NAME}_R2.txt >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
mv ${SAMPLE_NAME}_R1.txt ${SAMPLE_NAME}/
mv ${SAMPLE_NAME}_R2.txt ${SAMPLE_NAME}/
echo Moving fastq files to analysis directory complete >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo -------------------------------------------------------- >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log

# In the following step we will rename the data files to the required tophat read ID format "_1.fa" or "_2.fa"

echo >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo Renaming text files to match required tophat format >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log

cd ${SAMPLE_NAME}
#Current Directory=SampleX

echo The following text files will be renamed: >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
for file in `ls *.txt`
do
echo $file >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
done
mv ${SAMPLE_NAME}_R1.txt ${SAMPLE_NAME}_1.txt 
mv ${SAMPLE_NAME}_R2.txt ${SAMPLE_NAME}_2.txt
echo Finished renaming files >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo -------------------------------------------------------- >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log

# In the next step we will get the line count of the two read files so percent aligned can be calculated after the fact

echo >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo Starting collect line counts process >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo ${SAMPLE_NAME}_1.txt contains the following number of lines: >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
wc -l ${SAMPLE_NAME}_1.txt >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo ${SAMPLE_NAME}_2.txt contains the following number of lines: >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
wc -l ${SAMPLE_NAME}_2.txt >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo Finished  collect line counts process >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo -------------------------------------------------------- >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log

#In the next step we will align the illumina text format files to the reference genome using Tophat

echo >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo Starting Step1 - TopHat Alignment >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo The following fastq files will be aligned: >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
for file in `ls *.txt`
do
echo $file >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
done
echo >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
#### cmd = tophat [options]* <index_base> <reads_1> <reads_2>
echo The following command will be run: >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log

##########################################################
##########################################################	
## Pound out tophat run variants to select variant needed

## VARIANT 1 - WITH GTF NO INDELS (GENE EXPRESSION RUN FOR CUFFLINKS ABUNDANCE CALCULATIONS)
echo tophat --mate-inner-dist ${MATE_INNER_DIST} --mate-std-dev ${MATE_INNER_STD} --solexa1.3-quals --num-threads ${TOPHAT_CORES} --library-type fr-unstranded --GTF ${GTF_FILE} ${GENOME_REFERENCE} ${SAMPLE_NAME}_1.txt ${SAMPLE_NAME}_2.txt >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
tophat --mate-inner-dist ${MATE_INNER_DIST} --mate-std-dev ${MATE_INNER_STD} --solexa1.3-quals --num-threads ${TOPHAT_CORES} --library-type fr-unstranded --GTF ${GTF_FILE} ${GENOME_REFERENCE} ${SAMPLE_NAME}_1.txt ${SAMPLE_NAME}_2.txt

## VARIANT 2 - WITH GTF ALLOW INDELS OF DEFAULT SIZE (MUTATION CALLING)
#echo tophat --mate-inner-dist ${MATE_INNER_DIST} --mate-std-dev ${MATE_INNER_STD} --allow-indels --solexa1.3-quals --num-threads ${TOPHAT_CORES} --library-type fr-unstranded --GTF ${GTF_FILE} ${GENOME_REFERENCE} ${SAMPLE_NAME}_1.txt ${SAMPLE_NAME}_2.txt >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
#tophat --mate-inner-dist ${MATE_INNER_DIST} --mate-std-dev ${MATE_INNER_STD} --allow-indels --solexa1.3-quals --num-threads ${TOPHAT_CORES} --library-type fr-unstranded --GTF ${GTF_FILE} ${GENOME_REFERENCE} ${SAMPLE_NAME}_1.txt ${SAMPLE_NAME}_2.txt

##########################################################
##########################################################	

## This creates and subfolder called "tophat_out/"
## This folder will contain:	accepted_hits.bam (is it sorted?)
##								deletions.bed
##								insertions.bed
##								junctions.bed

#In the next step we will rename the alignment files
echo >> ../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log

cd tophat_out/
#Current Directory=SampleX/tophat_out

mv accepted_hits.bam ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}.bam
mv deletions.bed ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_deletions.bed
mv insertions.bed ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_insertions.bed
mv junctions.bed ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_junctions.bed

echo Finished Step1 - TopHat Alignment >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo -------------------------------------------------------- >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log

#In the next step we will calculate abundance estimates using cufflinks

echo >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo Starting Step2 - Cufflinks Abundance Calculation >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo Expression estimates will be calculated from the following tophat alignment file: >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
for file in `ls *.bam`
do
echo $file >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
done
#### cmd = cufflinks [options] <hits.bam>
echo The following command will be run: >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
for file in `ls *.bam`
do
echo cufflinks --quiet --num-threads ${TOPHAT_CORES} --GTF ${GTF_FILE} --output-dir ../cufflinks_out/ --reference-seq ${GENOME_REFERENCE}.fa $file >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
done
echo >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
for file in `ls *.bam`
do
cufflinks --quiet --num-threads ${TOPHAT_CORES} --GTF ${GTF_FILE} --output-dir ../cufflinks_out/ --reference-seq ${GENOME_REFERENCE}.fa $file 
done

## This creates a subfolder called "cufflinks_out/" in the sample directory
## This folder will contain:	genes.expr
##								transcripts.expr
##								transcripts.gtf

#In the next step we will rename the expression estimate files

cd ../cufflinks_out/
#Current Directory=SampleX/cufflinks_out

mv genes.expr ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_${PROTOCOL_TAG2}_genes.expr
mv transcripts.expr ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_${PROTOCOL_TAG2}_transcripts.expr
mv transcripts.gtf ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_${PROTOCOL_TAG2}_transcripts.gtf

echo Finished Step2 - Cufflinks Abundance Calculation >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo -------------------------------------------------------- >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log

cd ../tophat_out/
#Current Directory=SampleX/tophat_out

#In the next step we will sort the tophat result file with picard sort so the duplicate reads can be marked

echo >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo Starting Step3 - Picard SortSam process >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo The following BAM file will be sorted: >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
for line in `ls *.bam`
do                                                                     
echo $line >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
done
for line in `ls *.bam`
do
java -Xmx2g -jar ${PICARD_PATH}/SortSam.jar INPUT=$line OUTPUT=${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_PicardSorted.bam SORT_ORDER=coordinate TMP_DIR=/scratch/jkeats/temp/
done
echo Finished Step3 - Picard SamSort process >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo -------------------------------------------------------- >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log

#In the next step we will mark the duplicate reads in the BAM file produced by picard SamSort.jar

echo >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo Starting Step4 - Picard MarkDuplicates process >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo Duplicate reads in the following BAM file will be marked: >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
for line in `ls *_PicardSorted.bam`
do                                                                     
echo $line >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
done
for line in `ls *_PicardSorted.bam`
do                                                                     
java -Xmx2g -jar ${PICARD_PATH}/MarkDuplicates.jar INPUT=$line OUTPUT=../bamfile_dupsmarked/${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_PicardDupsMarked.bam METRICS_FILE=../bamfile_dupsmarked/${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_PicardDupsMarked_Metrics.txt REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT TMP_DIR=/scratch/jkeats/temp/
done
echo Finished Step4 - Picard MarkDuplicates process >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo -------------------------------------------------------- >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log

rm ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_PicardSorted.bam

cd ../bamfile_dupsmarked/
#Current Directory=SampleX/bamfile_dupsmarked
 
#In the next step we will index the BAM file for fast access and viewing in the IGV browser

echo >> ../..${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo Starting Step5 - Samtools BAM indexing process >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo The following BAM files will be indexed: >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
for line in `ls *.bam`
do                                                                     
echo $line >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
done
for line in `ls *.bam`
do                                                                     
samtools index $line
done
echo Finished Step5 - Samtools BAM indexing process >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo -------------------------------------------------------- >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log

#In the next step we will generate mapping statistics using samtools

echo >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo Starting Step6 - Samtools flagstat process >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo Mapping statistics will be generated from the following BAM file: >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
for line in `ls *.bam`
do                                                                     
echo $line >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
done
for line in `ls *.bam`
do                                                                     
samtools flagstat $line > ${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_SamtoolsMappingStats.txt
done
echo Finished Step6 - Samtools flagstat process >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo -------------------------------------------------------- >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log

#In the next step we will generate mapping statistics using picard

echo >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo Starting Step7 - Picard CollectAlignmentSummaryMetrics process >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo Mapping statistics will be generated from the following BAM file: >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
for line in `ls *.bam`
do                                                                     
echo $line >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
done
for line in `ls *.bam`
do                                                                     
java -Xmx2g -jar ${PICARD_PATH}/CollectAlignmentSummaryMetrics.jar INPUT=$line OUTPUT=${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_PicardMappingStats.txt VALIDATION_STRINGENCY=SILENT REFERENCE_SEQUENCE=${GENOME_REFERENCE}.fa ASSUME_SORTED=true IS_BISULFITE_SEQUENCED=false
done
echo Finished Step7 - Picard CollectAlignmentSummaryMetrics process >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo -------------------------------------------------------- >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log

#In the next step we will generate mean quality by cycle distribution plots using picard

echo >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo Starting Step8 - Picard MeanQualityByCycle process >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo Mean quality by cycle plots will be generated from the following BAM file: >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
for line in `ls *.bam`
do                                                                     
echo $line >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
done
for line in `ls *.bam`
do                                                                     
java -Xmx2g -jar ${PICARD_PATH}/MeanQualityByCycle.jar INPUT=$line OUTPUT=${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_PicardQualByCycle.txt CHART_OUTPUT=${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_PicardQualByCycle.pdf VALIDATION_STRINGENCY=SILENT
done
echo Finished Step8 - Picard MeanQualityByCycle process >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
date '+%m/%d/%y %H:%M:%S' >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log
echo -------------------------------------------------------- >> ../../${SAMPLE_NAME}_${GENOME_NAME}_${PROTOCOL_TAG}_${ALIGNMENT_TYPE}_run.log

#The run is complete

**bioinfosm** · 04-28-2011, 07:41 PM

Hey, tried galaxy for some or all of this? http://main.g2.bx.psu.edu/
Its getting really popular with a lot of groups, and a lot of tools are in-built

**Jon_Keats** · 06-21-2011, 09:37 PM

I've tried it a couple of times and it is clearly improving rapidly. Seems like a great place to start for people that are not overly comfortable with command line steps, particularly people looking to get expression estimates from their RNAseq samples with Tophat/Cufflinks/Cuffmerge/Cuffcompare. I would recommend a local install for most people so you don't have to transmit data.

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