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Old 03-03-2015, 07:38 AM   #19
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

The presence of an XS auxiliary tag doesn't mean that an alignment isn't unique (n.b., "unique" isn't really a useful term, there's a reason for MAPQ scores). bowtie2 should only count an alignment as not unique if the XS and AS scores are the same.

Note that you're typically best off simply filtering by MAPQ score.
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