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Old 11-13-2009, 11:20 AM   #4
amcrisan
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Location: Canada

Join Date: Oct 2009
Posts: 9
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As I understand it, the non-unique reads will not necessarily be discarded. They will be placed asides and may be resolved at later steps using Mosaik sort (the -rmm option). If you don't choose to do this, then I think the reads are essentially discarded.
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