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Old 07-05-2012, 04:41 PM   #8
sehrrot
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Location: USA

Join Date: Jul 2010
Posts: 58
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Hi EvilTwin

I think so. I am still waiting my pipeline for on-target rate and coverages. Duplicate level on Picard is around 20-25%, which is lower than FastQC one but higher than previously I've seen in the NimbleGen exome V2 (which as around 5-8%). I've done NimbleGen V3 exome with pre-multiplexing as I've done this for V2 as well (the performance actually same between pre-multiplexing and post-multiplexing; I've tested with NimbleGen, Illumina and also compared with Agilent post-multiplexing) and got the nice result. I am still not sure why the duplicate level is high ..

Anyway thanks for your reply.
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