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Old 04-13-2012, 07:36 AM   #1
Location: Ireland

Join Date: Sep 2011
Posts: 86
Default Unexpected FastQC results

Hi all, I was wondering if anyone could suggest an explanation for the somewhat weird FastQC results we got on our last run (human exome samples, Nimblegen v2 enrichment kit, 10 samples per lane at 2x100bp on a HiSeq 2000 with Version 3 chemistry). These are paired-end of reads from the same lane - all samples in the same lane showed this same pattern, though all of those samples were prepped at the same time too. The first reads seem completely fine but the second ones tank in quality around position 15-19. We did all sample prep in-house but we outsourced the sequencing (since we don't have a HiSeq on site).

The reads also showed some moderate sequence duplication (~21%) and an AT-bias, both of which I presume are caused by over-amplification during sample prep, so I'm going to tone down that in future. I still feel like that doesn't explain the weird quality drop here though. Can anyone suggest what it might be caused by?

Last edited by Rocketknight; 04-13-2012 at 07:38 AM.
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