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  • 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.

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

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    • #3
      Thanks, nilshomer!

      RNA-seq using HiSeq.

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

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