CisGenome -- an integrated tool for ChIP-seq data analysis

[Ghosh]

please help

When i am installing the cisgenome in Linux its giving me thease errors!
Do anybody know how to get rid off that? Thnaks!

./cpp/tablesorter.cpp: In function 'bool tablefile_sort(std::string, std::string)':
./cpp/tablesorter.cpp:77: error: 'fopen' was not declared in this scope
./cpp/tablesorter.cpp:91: error: 'fgets' was not declared in this scope
./cpp/tablesorter.cpp:100: error: 'fprintf' was not declared in this scope
./cpp/tablesorter.cpp:164: error: 'printf' was not declared in this scope
./cpp/tablesorter.cpp:169: error: 'fprintf' was not declared in this scope
./cpp/tablesorter.cpp:183: error: 'fclose' was not declared in this scope
./cpp/tablesorter_str.cpp: In function 'bool tablefile_sort(std::string, std::string)':
./cpp/tablesorter_str.cpp:77: error: 'fopen' was not declared in this scope
./cpp/tablesorter_str.cpp:91: error: 'fgets' was not declared in this scope
./cpp/tablesorter_str.cpp:100: error: 'fprintf' was not declared in this scope
./cpp/tablesorter_str.cpp:171: error: 'printf' was not declared in this scope
./cpp/tablesorter_str.cpp:176: error: 'fprintf' was not declared in this scope
./cpp/tablesorter_str.cpp:187: error: 'fclose' was not declared in this scope

[Ghosh]

How to convert a bowtie2 aligned .sam file to .aln file? please reply as soon as anybody can

[asiangg]

If you are looking for comparison between two conditions each with biological replicates, you can try out diffReps? Its automated pipeline allows you to analyze an entire ChIP-seq dataset in one command.

Hello,

My question is - how does the peak caller functions when i use 2 replicates and e.g. 1 input control. Will it call peaks for every replicate independently against the control and output the peaks which share both replicates? What will be happen if i use 2 replicates and 2 controls, lets say one input control and one IgG control?

Unfortunately, i could not find any explanation in the www how seqpeak exactly works and how it will handle more than the standard 2-sample analysis (ChIP+control). It is clear that i can call peaks for both replicates independendly but it would be beneficial if SeqPeak could handle e.g. replicats and different controls for the same ChIP-seq experiment in a single peak calling step.

Thanks, tec

[tec]

CisGenome v2 - SeqPeak

Hello,

used Cisgenome v1 (linux) for 2-sample (ChIP+Control) TF ChIP-Seq analysis. Now i switched to v2 (linux) and the new and recommended SeqPeak 2-sample peak calling.

My question is - how does the peak caller functions when i use 2 replicates and e.g. 1 input control. Will it call peaks for every replicate independently against the control and output the peaks which share both replicates? What will be happen if i use 2 replicates and 2 controls, lets say one input control and one IgG control?

Unfortunately, i could not find any explanation in the www how seqpeak exactly works and how it will handle more than the standard 2-sample analysis (ChIP+control). It is clear that i can call peaks for both replicates independendly but it would be beneficial if SeqPeak could handle e.g. replicats and different controls for the same ChIP-seq experiment in a single peak calling step.

Thanks, tec

[AveragePhD]

Cisgenome error message

Hi hji,

I was trying to do ChIP-Seq analysis with the sample data sets in the tutorial for 2 sample ChIP-seq. I am using Cisgenome v2 for windows but I got the error message "cannot write parameters to argument file!" when I used "Two sample peak calling (New and recommend)".

Can you tell me what might have caused this problem and how I can fix it?

Thank you very much for your help.

[tellam]

opening BAR files

A simple question - how can you open a BAR file?
Thanks
Ross

[Bas]

Hi Mudshark,

I was hoping to use the windows GUI for visualizations, I already have the core program running under OSX.


Thanks,

Bas

[mudshark]

why not running it under OSX natively, i.e. Darwin??

[Bas]

Hi all, I'm new here and am hoping someone may be able to help me out with a little Cisgenome issue I'm having. I've used Cisgenome successfully on a PC running Windows XP, but I'm now trying to run the program on my MacBook Pro using the Parallels program, which allows me to run Windows XP. I'm able to open the program through XP on my MAC and can load files as well, but when I try to run an application (right now I'm attempting Gibbs sampling) I get the quickly flashing black window that then disappears, and the program won't continue running. I have checked the file paths and file names, and there are no blank characters included anywhere. Also, the cisgenome.ini file does specify the correct Cisgenome installation path, so I'm at a loss as to what the problem is. Does anyone have experience running Cisgenome on Windows XP through MAC Parallels? Or perhaps it isn't possible to run the program this way. Thanks in advance, any assistance will be greatly appreciated.

Hi everybody, I just started using Cisgenome and was hoping to run it on my Mac using Parallels. However, I'm experiencing similar problems and was hoping anybody has a clue how to overcome this issue?

Cheers,

Bas

[honey]

I agree cisgenome is probably created by a lInux reseacher and they never cared it has to be used by biologists. I wasted lot of time and end up using Cistrome they need to look into that. They even dont respond emails. That is bit annoying.... sorry but it is true.. If you can not support community then take off your software from public claims

[gntc]

Does anyone know why when running One Sample Peak Calling Peak Detection with Boundary Refinement and Single Strand Filtering selected no .cod file is created? When I run this with my data I get 6 new files:

title.bar
title.cgw
title_F.bar
title_F.cgw
titlle_R.bar.tmp
title_R.regtmp

The .tmp files suggest to me that maybe the program is crashing. Has anyone else experienced this?

[gntc]

yes dear, I am doing extactly the same

but cisgenome(windows version) seems not like my PC, so I switched to linux version on our cluster and it worked.

I wonder it might be a bug of windows version.

Haha, yes dear.

The windows version is buggy and annoying. Good to know that I'm not the only one doing what I'm doing and having problems with the windows version.

[townway]

yes dear, I am doing extactly the same

but cisgenome(windows version) seems not like my PC, so I switched to linux version on our cluster and it worked.

I wonder it might be a bug of windows version.

Honey,

You can convert like this:

BAM -> BED -> ALN

Then use the ALN file with the peak calling to get a BAR file. I use the bedtools package to convert bam to bed and cisgenome to convert bed to aln.

[gntc]

Honey,

You can convert like this:

BAM -> BED -> ALN

Then use the ALN file with the peak calling to get a BAR file. I use the bedtools package to convert bam to bed and cisgenome to convert bed to aln.

[townway]

Hi all,

I am using latest Cisgenome (windows version) to call Chi-seq peaks. But I got the errors when I used "Two sample peak calling (New and recommend)". After I added my IP and input file in aln format and used default setting, I got the error window "cannot write sample list to argument file!"

Would you tell me what the problem is ? I also tried the demo data, the same happened.

Thank you so much

Wei