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Old 04-16-2020, 01:40 PM   #5
Junior Member
Location: Rochester, NY

Join Date: Feb 2020
Posts: 7

Ah I figured out what was happening. Your comment about the high Phred scores got me thinking on the right track. After looking at the documentation further it seems that bbmap has a flag to cap base quality which is set to 41 by default, which would eliminate almost all of my bases, explaining my results.

I added the following flags

maxcalledquality=1000 ibq

to remove the cap on quality score and also 'ibq' to ignore any base scores it might consider problematic in case they are still being flagged somehow. This fixed my issue and outputted a properly trimmed file.
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