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  • bwa multiple alignment

    Hi Guys,
    a question about multiple alignment with bwa and coverage. Let's say I use the flag -n 2 when running bwa samse and for a couple of (not necessarely mated ) reads I get the following situation

    read1: maps on region A and in XA report a second alignment on region B
    read2: maps on region B and in XA report a second alignment on region C

    When I run the pileup of this alignment file (e.g. with samtools) will I get a coverage 2 on region B?

    thanks for helping

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