I am intrigued by this trend of my illumina reads. The forward reads for every genomic DNA sample show a good per base sequence quality (mostly Q 25-30) even towards the last base (150 bp), while the file containing reverse reads shows a drop of upto Q 12. I see this trend in all my read files and am confused about what goes wrong when the sequencing guys perform the reverse read sequencing.
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deepti1rao •
The quality for read #2 is typically worse than for read #1. Having said that, a drop of 12 is a bit much for 150 base reads, you typically only see large decreases with 250 base long rapid runs on HiSeq 2500s. It's possible that there was a technical issue late in the run, ask the people that run the machine. On the plus side, the quality still sounds OK for most uses.
Can you elaborate on this: The quality for read #2 is typically worse than for read #1.????
There's no elaboration needed, that's generally the case for Illumina sequencers.
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