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Old 06-26-2012, 12:53 AM   #4
EvilTwin
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Location: Heidelberg

Join Date: Jul 2011
Posts: 8
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Hi sehrrot,

how do you exactly calculate your on-target and coverage data? Maybe I can learn something :-)

We tried the SeqCap EZ 3.0 and got ~ 70x average coverage per Exome when pooling 4 samples on an Illumina HiSeq 2000 lane (GATK DoC Walker), with ~ 60 % bases strictly on-target (Picard CollectHSMetrics with the supplied "capture.bed" as target/bait file).

I had a talk with some Roche/Nimblegen guys a while ago, and they stated that Nimblegen calculate their on-target values by defining anything within 150 bp +/- the target regions as on-target, which of course increases that value. Also, the primary focus in developing SeqCap V3 was to increase the target region size, while it is allegedly very hard to increase the on-target efficiency. So I would not expect that there is much difference to V2 in that respect.
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