I have a batch of recent HiSeq paired end runs where the sequencing centre reported pre-phasing problems on one or both reads of some runs due to reagent issues. Should I expect to see this reflected in poorer quality scores in the FASTQ earlier in the reads? Basically I am trying to figure out how to recover usable data from the problem runs. I think that trimming + a quality filter should be ok if the pre-phasing is reflected in the quality scores the way I expect, but I am not familiar enough with the technology to be confident. Can anyone confirm if this is the right way to go?
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