QC on Encore Rapid Libraries

[njain]

Hello everyone! I am very new to NGS and have recently started generating libraries using the Encore Rapid DR library system. All was well until we sent our samples to the core for sequencing. The first red alert was that we got unusually high Picogreen reads. Second, they all failed qPCR analysis. The qPCR was performed using the p5 and p7 illumina primers--> the core considers anything that has more than a 3 cycle difference from PhiX standard a fail.

I was wondering if anyone else had run into similar problems and what kind of QC was being done for Rapid libraries. My understanding is that comparison to PhiX standards is not suitable because the Encore Rapid libraries are not PCR enriched.

Thanks!

Nitya.