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  • Chiper
    Member
    • Dec 2009
    • 13
    #1

    Long peak length from ChIP-seq data

    Hi All,
    I am new to this forum. I have recently started using AB Solid V 2.0 for ChIP seq of a Drosophila TF. I used 500 bp avg Chromatin for pull down and during the library prepn it was brought down to ~100-200bp.

    We ran MACS with default parameters on the data. I was surprised to see that mean peak length for Test IP vs.Input was ~1.6 Kb! There were peaks as big as 10 Kb at times. Is this common? How can I get better resolution? Please help!
    Tags: None
    • snetmcom
      Senior Member
      • Oct 2008
      • 159
      #2
      this is an excellent question that I would like more insight on as well. I have CHiP in my future.

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