[Bas]

Hi Mudshark,

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


Thanks,

Bas

[tellam]

opening BAR files

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

[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.

[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

[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

[Ghosh]

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

[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