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  • elena.zaslavsky
    Junior Member
    • Mar 2014
    • 1

    #1

    Unmapped reads (ChIP vs Input)

    I'm analyzing a ChIP-seq (Illumina) experiment, and getting very different proportions of unmapped reads (bowtie2) from the ChIP (~35%) and input (~5%) sampes. This holds true for all the replicates and all the conditions. Any ideas why?
  • Chipper
    Senior Member
    • Mar 2008
    • 323

    #2
    Probably more adaptor dimers in the ChIP, if the input was prepared with more DNA, or since it holds for all samples you might have a contamination from the ChIP reagents. It shouldn't matter but you can always do a de novo assembly with the unmapped reads if you really want to know.

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