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  • dizhang
    Junior Member
    • Jan 2010
    • 2
    #1

    Maq -u parameter

    Hi guys,

    -u FILE Dump unmapped reads and reads containing more than nmis mismatches to a separate file [null]

    When I set this parameter in maq for paired alignment, the dump files cannot distinguish between the two pairs and assign them the same name (Eg. Gene1/1 and Gene1/1 instead of Gene1/1 and Gene1/2). Is there a way to get proper .dump file format for paired-end alignments?

    Thanks!
    Tags: None
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