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  • 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?

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

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