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  • Number of mismatches in Bowtie

    Hi all,

    Bowtie's manual says the following about -v mode:
    "-v <int> Report alignments with at most <int> mismatches"

    I understood from this that for paired end reads the whole alignment, including both ends, will contain up to <int> mismatches.

    But when I ran my data with -v 2 mode I got the following MD:Z values for 2 ends of the same read:
    23A3A36
    59T3T0

    and another example:
    32A13G17
    15A21A26

    So it seems like 2 mismatches are allowed per end.

    Just wanted to make sure that this what -v means, and that I didn't do something else that caused this.

    Thanks,
    Rachelly.

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