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FelixKrueger / TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
GNU General Public License v3.0
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equivalent of `--discard-untrimmed` parameter in `trim_galore` #138

Closed bounlu closed 2 years ago

bounlu commented 2 years ago

What is the equivalent of --discard-untrimmed parameter in trim_galore? How can I discard the reads without the adapter sequence from the output for the downstream analyses?

cutadapt:

  --discard-untrimmed, --trimmed-only
                        Discard reads that do not contain an adapter.
FelixKrueger commented 2 years ago

I don't think there currently is an option to discard reads without an adapter sequence. I suppose as a little 'hack' you could set -q 0 to skip quality trimming, and set --max_length (readlength) - 1. In theory this should do the same thing.