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Old 09-30-2016, 01:34 PM   #1
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Question Batch bias while merging TrueSeq PCR-free and Nano data

Hi All,

We are starting a new sequencing project of human DNA samples. Part of our sample was already sequenced using Illumina TrueSeq PCR-free kit. Now, it turned out that part of the new samples does not qualify for PCR-free protocol and we were suggested to switch them to TrueSeq Nano protocol. In addition, we have been advised that PCR-free protocol could have a big failure rate during library prep currently, up to 15%. The issue seems to be connected to changes in kit chemistry and affects many labs worldwide.

However, I am a little bit worried about the possible extent of batch bias arising when processing/merging data from two different protocols (PCR-free and Nano). Does anybody here have this kind of experience?

Thank you in advance!
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