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Old 03-03-2015, 08:47 AM   #21
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

Therein lies the problem, there is no single definition of "uniqueness". There are multiple incompatible definitions. Further, if we relax the --score-min settings enough then by some definitions there will never be any unique alignments. This is why MAPQ is a generally more useful concept and you'd be better served just forgetting about the term "unique" in this context.
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