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.
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.