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Old 09-27-2012, 12:55 AM   #1
Location: Germany

Join Date: Jan 2011
Posts: 14
Default Exome Sequencing with nimblegen SeqCap EZ v3


we working with a GAllx from Illumina and have good experience with nimblegen SeqCap EZ v2 (on target).
We compare the nimblegen SeqCap EZ v3 and Illumina TrueSeq exome kits and the results shocked me .
For nimblegen we have nice mapping rate and low duplication level, but on target it is only 30 %.
For illumina mapping is well but duplicate level is high (20 - 30 %). On target we can reach 76 %.

How it could be that the on target of nimblen v3 kit is so bad? We have good results in the pre steps and everything looks similar to nimblegen v2.

About hints or sharing experience about the nimblegen v3 kit I would be very lucky.
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