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  • unidodo
    Junior Member
    • Jul 2010
    • 8

    #1

    not uniquely mapped reads

    We got a large fraction (70%) of not uniquely mapped reads. Just wondering if anyone knows the possible cause?

    Thanks in advance.
  • nilshomer
    Nils Homer
    • Nov 2008
    • 1283

    #2
    What experiment, what technology? Please be verbose in your answer!

    Comment

    • unidodo
      Junior Member
      • Jul 2010
      • 8

      #3
      Thanks, nilshomer!

      RNA-seq using HiSeq.

      Seems that majority of not uniquely mapped reads come from either one chromosome or mitochondrion genome.

      Comment

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