[hji]

How to choose one-sample chip-seq cutoff

In the output of windowsummaryv2, go to the last column (negbinomial_exp/obs), find the first line with value < 0.1 (i.e. FDR < 10%), then go to the first column of this line, find the number c, use c as your cutoff. In the user manual webpage, you can find an example summarys1.txt in section 3.4. In this example, you will go to this line:

8 750 0.000024 0.000000 0.000000 0.000001 0.048812

The cutoff is 8.

[Husen]

Cutoff value for analyzing on-sample chip-seq data

Hi hji,

Could you please explain briefly how to set cutoff value (-c option) of the peak-detector for analyzing one-sample chip-seq data.

Based on section 3.4 of the user manual, FDR for each read count is given in output of windowsumarryv2 and the peak-detector is supposed to set a single value for the cutoff (-c) option. I wonder how this could be done or the default value (10) would be fine?

your answer is highly appreciated..

[hji]

Husen,

Thanks for providing a solution.

Hi,

I had a problem to execute cisgenome-2.0 under Linux (Ubuntu 10.10), but including the following package in tablesorter.cpp and tablesorter_str.cpp solved the problem.

#include <cstdio>

regards

[Husen]

can't build cisgenome from source code or can't execute it on Linux system

Hi,

I had a problem to execute cisgenome-2.0 under Linux (Ubuntu 10.10), but including the following package in tablesorter.cpp and tablesorter_str.cpp solved the problem.

#include <cstdio>

regards

[hji]

To tir_al

You don't need to choose a species/genome in v2 (seqpeak). The program will automatically determine the number of chromosomes and chromosome length. This way, it can be applied to all species. After you run the program, you get bar files, you then visualize those bar files with the genome annotation you want to use.

[tir_al]

Cisgenome V2 Genome selection

Dear Hji,

Could you please tell me in which way to choose the appropriate genome for my samples in cisgeome v2 on linux os?

I couldn't find the flag in the seqpeak application.

Reagards.

[hji]

cisgenome v2.0

We have just updated cisgenome to v2.0. BAR->Wig conversion is added. Two-sample ChIP-seq analysis algorithm updated which solves most of the memory problems we had previously.

[Husen]

cisGenome output (.bar or .cod) to .wig?

Anyone know of a utility to convert .bar files to .wig files?

I'd be happy to write a program to do it - but any pointers for the .bar format would be helpful. I'm sure I'm not the only one who would be interested in seeing cisGenome output in the UCSC genome browser (which doesn't read .bar last I checked).

I need a similar program to convert sicGenome output (bar/cod) to wig, please let me know if you have got/developed such a tool.

[Husen]

I had some compilation problems related to 32/64 bit later on for ./cpp/tablesorter.cpp and ./cpp/tablesorter_str.cpp - I had to remove the "-m64" flag for the two targets before being able to compile. Just in case you get the same problem later on. Please be aware that I did not test if this has an effect on the results.

Cheers,
Holger

Thanks for mentioning the CPU solution, it helped me a lot.

[Husen]

Hi lqscici,

the problem is that the file "makefile" in cisgenome_project is not a file in proper Makefile format as a standard "make" command would expect it, but it's a shell script.
You can try a

./makefile

in the cisgenome_project folder (should work because of the "#! /bin/sh" in the first line), or you call it explicitely as a shell script:

sh makefile

I had some compilation problems related to 32/64 bit later on for ./cpp/tablesorter.cpp and ./cpp/tablesorter_str.cpp - I had to remove the "-m64" flag for the two targets before being able to compile. Just in case you get the same problem later on. Please be aware that I did not test if this has an effect on the results.

Cheers,
Holger

Thanks for mentioning the CPU solution, it helped me a lot.

[hathiram]

hello everybody, I am using cisgenome for chip-chip data analysis. I am getting constant FDR .619523 for all ~900 potential binding regions in .cod file, using two sample analysis in TileMap, where I put sample > control.
can anybody tell me that why i m getting constsnt FDR for all 900 regions.

i willbe really highly thankful to all.

[hathiram]

hello, i am using cisgenome for chip-chip data analysis.

[hklein]

compile cisgenome

Hi lqscici,

the problem is that the file "makefile" in cisgenome_project is not a file in proper Makefile format as a standard "make" command would expect it, but it's a shell script.
You can try a

./makefile

in the cisgenome_project folder (should work because of the "#! /bin/sh" in the first line), or you call it explicitely as a shell script:

sh makefile

I had some compilation problems related to 32/64 bit later on for ./cpp/tablesorter.cpp and ./cpp/tablesorter_str.cpp - I had to remove the "-m64" flag for the two targets before being able to compile. Just in case you get the same problem later on. Please be aware that I did not test if this has an effect on the results.

Cheers,
Holger

[lqscici]

Hello,

I am a rookie in applying cisgenome and now I have a problem in installing it in Linux. I have unzipped cisgenome v1.2 and entered the "cisgenome_project", after typing "makefile" it appears "-bash: makefile: command not found". If I change to run "make", I get the error "makefile:3: *** missing separator. Stop."

I don't know what to do, I have been searching through manuals and forums for weeks now. Any help would be greatly appreciated!

Thanks!

[honey]

to find binidng motif in chip on chip data

I have nimblegen Chip on chip data with two antibodies and want to find out common binding motif from the data could anyone point me how to proceded I know there are several softwares -chipmotif, cisgenom etc.
The file I have has chr position marked 1000 bp (I combined probles of different regions) and then log ratio of intensities. How to create intial file meaning Bed or else. Do I have to put these chr positions in data in USCS genome browser to get seq out put but then what will happend to score. Apology fro asking such a trivial question.