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Old 08-06-2011, 07:13 PM   #6
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Location: East Coast, US

Join Date: Jun 2010
Posts: 177


Fastqc and picard work at different levels. Fastqc works on the read level - it takes the read sequences and estimates the duplication level. Picard works on the alignment level - as already explained, it also considers the location of the read (and its mate if applicable). So it depends what you are looking for. As far removing PCR-introduced duplicated reads, picard definitely is more relevant.
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