Use `--action=lowercase` for short reads but keep trimmed passed reads.

[y9c]

Is it possible to keep the original sequence for discarded reads for debugging, but trimmed the reads that passed the length filter? Thank you.

[marcelm]

Do I understand correctly that you want --action=lowercase for reads that are sent to the --untrimmed-output file, but the normal behavior for trimmed reads?

No, this isn’t possible at the moment. It is also a bit hard to add this because the check whether a read should be filtered is done when the action has already been applied to it. So when the read is written out, it’s already trimmed and one would somehow have to add back the bases and turn them into lowercase.

[y9c]

Thank you for the information.