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Old 10-15-2012, 06:34 AM   #8
advancing one byte at a time!
Location: Bangalore, India

Join Date: Jun 2011
Posts: 56

I had the same query. What i personally feel is that Picard is more accurate.

My reassoning is that fastqc is calling around 70% duplication looking at only the read 1 file and a similar amount using the read 2 file without using any information on the mapping.
Picard on the other hand looks at teh mapping and uses both start and end regions of the fragments to call duplicates which logically makes more sense, right? Fragments starting at the same position but ending at varying ones can't be seen as duplicates and discarded IMHO!
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