Better to risk low concentration library or further amplification?

[krobison]

Here's an issue which has arisen with some SureSelect processed libraries for the Illumina: after the hybridization the amount of library is barely within spec -- hence my question about quantitation.

So, the question is which path to take: push the libraries forward as is, with a risk of missing peak sequencer yield due to suboptimal cluster density, or run a few more (how many?) cycles of PCR to increase the concentration but also up the odds of getting PCR duplicates?

[NextGenSeq]

It worked fine for me and I could barely detect it on my Nanodrop. We are in the process of evaluating the Kapa Q-PCR kit which I think the Broad Institute has switched to.

[GW_OK]

Check out this thread.
You can prep a flowcell with a library that is <100pM with no problems.

[lh3]

No, I think the expected PCR duplicate rate is irrelevant to the PCR cycles. The duplicate rate is determined by the number of molecules before amplification.