We just finished a GAIIx 76 X 2 PE run of libraries prepared with Agilents Whole exome Sure Select kit. We analysed them using the Illumina Pipeline and aligned them to the human genome. The overall error rate was ~1% but when I look at the error plots the error rate increases rapidly to 5% starting at ~65 cycles on both reads. We looked at the RTA runtime stats charts for the quality and focus and nothing seems to go bad for either read. Has anyone using Exome Capture observed this? Could it be an alignment issue? I was wondering if we may be starting to sequence into the other adapter?
Thanks
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