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Old 08-05-2011, 05:52 AM   #2
Location: Germany

Join Date: Mar 2011
Posts: 68

Hi fabrice,
I am not sure, but I think fastqc counts all identical reads as a duplicate. In comparision to that, picard marks only these reads as duplicates, where the position of the forward and the reverse read is the same. So for Picard it is not enough, that for example just the forward reads is the same.
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