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  • aquleaf
    Member
    • Mar 2010
    • 38
    #1

    ChIP-Seq mapping rate

    Hi.

    We performed 36bp ChIP-Seqs in mouse and ran Bowtie to align the reads. Around 50% reads were not mapped. Is it reasonable? Does it mean our ChIP-Seqs were not successful?

    Wish your help! Thanks very much!
    Tags: None
    • rnaeye
      Member
      • May 2011
      • 80
      #2
      Originally posted by aquleaf View Post
      Hi.

      We performed 36bp ChIP-Seqs in mouse and ran Bowtie to align the reads. Around 50% reads were not mapped. Is it reasonable? Does it mean our ChIP-Seqs were not successful?

      Wish your help! Thanks very much!
      Hi,
      If these are uniquely mapped reads, I am not surprised. If they are non-unique, most likely it's because of sequencing run not your experiment.

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