View Single Post
Old 05-02-2016, 05:32 AM   #14
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,091
Default

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).
GenoMax is offline   Reply With Quote