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Old 07-06-2012, 04:05 AM   #10
sehrrot
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Location: USA

Join Date: Jul 2010
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Hi EvilTwin

Thanks for your sharing. I am guessing my sample would have the problem in sample prep or capture efficiency. Otherwise, it might be a problem in my HiSeq, as I've experienced in the dramatic quality drops after the cycle 80 and subsequently got a loss of cluster in read 2.

Anyway, apart from that, I think I got an answer why higher duplicate level in Fastqc than picard. FastQc find the identical sequences compared to others but they could be an enriched fragments, not solely for duplicates. Thus, Picard take information of paired end and if two sequences are identical as well as having the same start position of paired end sequences, Picard calls them as duplicates.
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