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Old 07-10-2012, 07:13 AM   #1
Location: New York

Join Date: Nov 2011
Posts: 19
Default PCR duplicates and reads mapping to multiple locations


I have a ChIP-seq library built from Truseq kit. The alignment by BWA looks reasonable, with 14,826,606 out of 19,875,610 mapped to mouse genome. But only 6,504,252 left after removing duplicates by Picard. Then I filtered out the reads mapping to multiple locations and only 731,693 reads left. I think there must be something wrong with my library prep. But what could be the reason? How can I avoid it?
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