Hello and good day.
I am teaching students using the Galaxy server tutorial “Reference-based RNA-Seq data analysis,” which uses Cutadapt for trimming. I would like to know: if my RNA-Seq dataset does not contain adapters but does have low-quality reads, how can I remove only the low-quality reads without trimming for adapters?
Greetings @mmomeni,
I don’t think CutAdapt has a --min-mean-quality kind of flag to use. But it does have error related filtering options like: --max-expected-errors ERRORS and --max-average-error-rate ERROR_RATE.
A description can be found in the documentation:
CutAdapt Docs
On Galaxy Europe these options can be found here:
Fastp however does have more quality based filtering options:
See: Fastp Docs
Hopefully this answer helps!
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