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Old 04-07-2013, 02:05 PM   #1
slny
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Location: FL

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Default CHIP-Seq analysis

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
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Old 04-08-2013, 04:57 AM   #2
Jluis
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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/anshul...e/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
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Old 06-22-2016, 01:49 AM   #3
SylvainL
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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?
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