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  • zhouzaiwei
    Junior Member
    • Sep 2013
    • 2

    #1

    how to report only 1 hit read by bowtie2?

    in bowtie1 there is a parameter -m 1 to report only 1 hit read, how to do this in bowtie2?
  • a_mt
    Member
    • Jul 2012
    • 34

    #2
    In bowtie2 if a read aligns to multiple locations it has XS tag. You can simply use sed to delete lines with this tag, if this is what you wanted.

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    • zhouzaiwei
      Junior Member
      • Sep 2013
      • 2

      #3
      thanks a lot, this is what i wanted.

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