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Old 05-02-2016, 05:32 AM   #14
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,091

If MarkDuplicates is working as expected then the duplicates on HiSeq 4000 are real optical dups likely formed by pad-hopping (contamination of nearby nanowells). For NextSeq 500 they probably come from one too many PCR cycles.

One possible cause of the duplicates in general is experimental origin (likely # of PCR cycles).
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