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  • amosine
    Junior Member
    • Oct 2011
    • 3
    #1

    What's wrong with my ChIP seq data?

    I perform H3K9me3 ChIP experiment and built the libarary acoording illumina's ChIP seq libarary protocol. The analysis of the data is as follows:

    raw read: 46891730
    map read: 42812364
    uniq read: 40442380
    used read:13409805
    map ratio: 91.30%
    uniq read: 86.25%
    used ratio:28.6%
    region: 253

    The used raed/used ratio/region is too low. I cannot figure out the problem, could anyone help me?? Thanks!
    Tags: None
    • kopi-o
      Senior Member
      • Feb 2008
      • 319
      #2
      More details, please. Where is your output coming from? What does "used ratio" refer to exactly?

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