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  • maq output

    Hi,

    I want to have a distribution of number of mismatches in mapped reads from .map file. (how many of mapped reads have 1 mismatch, how may have 2, etc.)

    it's a straight forward question, I'm guessing there is a a straight forward answer.
    I found pileup and mapcheck, but none of them gives me the information that I need.

    can any one help me with this?

    Thanks

  • #2
    mapview gives you the number of mismatches for each read (column 10 I believe)
    then:
    cut -f10 | sort | uniq -c

    Comment


    • #3
      thanks adam

      Comment

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