Has anyone noticed issues with quality scores on amplicon runs since the new version of bcl2fastq came out? I've had a number of runs be questionable since late Oct, but I also changed machines at the same time. Trying to figure out if I need to adjust wetlab conditions to new machine or if it's related to the software update.
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The beginning of R2 qscores are really low. This last run, R1 looks great with ~10% phiX aligned. R2 is horrible, <1% phiX aligned. I'm not sure how this would be software related but the thumbnails look fine-the machine didn't lose focus, clusters are there.
oh hadn't seen that paper, thanks. Haven't used bbmap but know it's on one of our clustersMicrobial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.
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Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.
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Originally posted by thermophile View PostHas anyone noticed issues with quality scores on amplicon runs since the new version of bcl2fastq came out? I've had a number of runs be questionable since late Oct, but I also changed machines at the same time. Trying to figure out if I need to adjust wetlab conditions to new machine or if it's related to the software update.
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