Whole Exome Capture

[Bruce E]

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

[kmcarr]

Bruce,

Your result sound quite typical to me. A rising error rate at the end of the read is expected and normal. 5% may be a little higher than I'd like but I'd be perfectly satisfied with that result. The rising error rate has to do with the falling intensity; the signal to noise ratio drops. Focus is not an issue here. Oh, and those Q values reported by RTA are complete fantasy, don't believe them.

[lmf_bill]

Bruce,

Your result sound quite typical to me. A rising error rate at the end of the read is expected and normal. 5% may be a little higher than I'd like but I'd be perfectly satisfied with that result. The rising error rate has to do with the falling intensity; the signal to noise ratio drops. Focus is not an issue here. Oh, and those Q values reported by RTA are complete fantasy, don't believe them.

nod
what about the 5 primer error rate, it seems due to primer.