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  • slny
    Member
    • Mar 2011
    • 54
    #1

    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
    Tags: None
  • Jluis
    Member
    • Apr 2012
    • 44
    #2
    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

    Comment

    • SylvainL
      Senior Member
      • Feb 2012
      • 180
      #3
      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?

      Comment

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