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Old 07-06-2012, 01:55 AM   #9
EvilTwin
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Location: Heidelberg

Join Date: Jul 2011
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Hi sehrrot,

Initially we also compared Agilent50MB post-capture multiplexing and NimbleGen V3 pre-capture multiplexing on the same set of samples, and there were no dramatic differences concerning duplication in that run (5 vs 6 %), but NimbleGen doing slightly better concerning on-target rate and also per-interval coverage (and naturally overall coverage due to the larger target size).
I checked some samples with FastQC, it also displays higher duplication levels, around 15-20 % (so perhaps much of it comes from unmapped reads?)

I will ask the sequencing core facility what exactly the problem was with the run displaying the exceptional high level of duplication
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