[bioinfosm]

good one Aaron! I keep using BEDTools more

[quinlana]

Use IGV to output plots of a region of a bam file with the following sample script

http://www.broadinstitute.org/igv/batch

attached is an example (note path to bam and snapshotDirectory need to be absolute not relative)

new
load myfile.bam
snapshotDirectory mySnapshotDirectory
genome hg18
goto chr1:65,289,335-65,309,335
sort position
collapse
snapshot

<shameless plug>
Note that BEDTools has a tool called bedToIGV that will automatically create an IGV batch script from a BED, GFF, or VCF file.
</shameless plug>

[arnoldliao]

IGV scripting function

Use IGV to output plots of a region of a bam file with the following sample script

http://www.broadinstitute.org/igv/batch

attached is an example (note path to bam and snapshotDirectory need to be absolute not relative)

new
load myfile.bam
snapshotDirectory mySnapshotDirectory
genome hg18
goto chr1:65,289,335-65,309,335
sort position
collapse
snapshot

[simonandrews]

Hi, simonandrews

I just noticed that the SeqMonk Release Notes talks about SeqMonk v0.12.0 but it seems I can only find SeqMonk v0.11.0 online. Do you know where to find v0.12.0?

Sorry, I'd failed to copy over the new version of the download page from our staging server. If you try again now the links should be in place (if you don't see them press shift+refresh in your browser to force a cache update).

Simon.

[natstreet]

I can see v0.11.0 listed at their website and if you swap 11 to 12 in the download URL there is something there to be downloaded

http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/seqmonk_v0.12.0.zip

[cliff]

Hi, simonandrews

I just noticed that the SeqMonk Release Notes talks about SeqMonk v0.12.0 but it seems I can only find SeqMonk v0.11.0 online. Do you know where to find v0.12.0?

Thanks

[drio]

I'd use circos and it's 2d tracks.

[natstreet]

This week I discovered that using BigWig files for coverage data works really nicely in GBrowse.

I would really love to have a simple plotting tool to take per chromosome coverage data from something like a BigWig file and plot a nice looking coverage figure. I'm thinking of coding it myself in (probably) python or (maybe) R but if anyone can point me to examples to get started that would be great. Although some genome browsers make coverage plots, they just don't look nice for publication use IMHO.

[cliff]

Hi, golharam and simonandrews

Thanks! I am using WinXP. I will try to run SeqMonk on my desktop first to see if it works.

-c

[ForeignMan]

Hi everyone,

IGV can also visualize the coverage of a whole chromosome at once without having to zoom in:
You need to create an extra .tdf-file (a binary tiled data file) using igvtools with the command "count" (see http://www.broadinstitute.org/igv/igvtools).

For example
igvtools count -z 7 -w 25 -e 0 alignments.bam alignments.coverage.tdf hg19

It supports the formats .sam, .bam, .aligned, .sorted.txt, and .bed.

Then you can load the .tdf-file into IGV and you get a pretty nice coverage plot.

[simonandrews]

hi, simonandrews

Do you have any experience in trying SeqMonk in linux?

If you're running Linux locally on your machine then what you tried should have worked (and we use that here very successfully).

As others have pointed out, if you want to run SeqMonk on linux from a remote system over SSH you'll need to make sure that your ssh session is started with an X tunnel available (either ssh -X or set the appropriate flags in PuttY) and that you have a local X server running on your machine. This is the same for all graphical linux programs.

Having said that, I'm not sure I'd encourage people to run SeqMonk this way. The nature of the program means that it does big complex updates to its display all the time, which means that it has to send an awful lot of display data over X to work remotely. We know of one site who do it this way, but they run an nx server to improve the display performance.

Really, SeqMonk is better run as a local native application. It's designed to work on modest hardware so you don't need a particularly powerful PC to run it (the default configuration is optimised for a dual core machine with 2GB of RAM). If you've not tried running it directly on your desktop I'd try that before going to the hassle of getting a decent remote connection working.

[golharam]

Are you using Windows? You'll need to install an X Server like ReflectionX, eXceed, or Cygwin. Googling for "X Forwarding on Windows" turned up http://www.cs.caltech.edu/courses/cs.../xwindows.html

[cliff]

cliff - Make sure you use -X for X11 forwarding with ssh

hi, golharam

How to use -X for X11 forwading with SSH? I am not familiar with X11. I turned on "Tunnel X11 Connections" in ssh settings but it didn't work..

[golharam]

cliff - Make sure you use -X for X11 forwarding with ssh

[cliff]

hi, simonandrews

Do you have any experience in trying SeqMonk in linux? I use SSH to connect our linux server. I just downloaded SeqMonk to my directory and tried to launch it by using

java -Xmx1500m -classpath $CLASSPATH:. uk.ac.bbsrc.babraham.SeqMonk.SeqMonkApplication

but it didn't pop up any window.. I was wondering what the correct way is to use SeqMonk in Linux.

Thanks

-c