CHIP-Seq analysis

[slny]

I'm very new in ChIP Seq data analysis.

Is there any CHIP Seq analysis pipeline that I can use? Any tutorial of CHIP Seq data analysis?

Thanks,
Slny

[Jluis]

Hi slny,

Have a look at this pipeline. It has been set up by the ENCODE project as a reference for ChIPseq analysis.

https://sites.google.com/site/anshulkundaje/projects/idr

By the way, I'd like to know which is the opinion of the bioinformatic analysts community about this particular ENCODE pipeline.



With best wishes

[SylvainL]

Hi, it's an old thread but I have a comment...

I had to re-run the same pipeline on the same ChIPseqs using actually the ENCODE guideline and I am facing something I didn't expect: I do not get the same results! Not by far but still different. Did you experience that? Can it be due to the idr step?