I have a 3kb Illiumina library which is contaminated with a higher than expected degree of PE reads (ca 250 bp). I've attempted to remove most of them up (it was about 50-60% of the reads) but some remain because the unitigger detects them
input: 14,800,608 pairs
InsertSizes()-- lib 5 mean 238 stddev 77 samples 1015048
is there any way I can ask the overlapper to discard such reads? are there any other recommendations (sort of not using the data)?
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