Suggestion: filter mode for polyA

[NickNCL]

Hi,

I'm using cutadapt v4.9 installed with conda

Maybe my aim is a bit niche here, but I'd like to filter out any reads matching the polyA filter in cutadapt (rather than trimming the polyA which is the default behaviour)

I was hoping that using --discard-trimmed in addition to --poly-a option would have this effect, but seemingly not

Input reads are all 50 bp, output contains shorter (trimmed) reads

This was my command:

(cutadapt4.4) nnb85@fms-302011:~/Ecoli_RNAP_pacing/Pamela/RawData/NoPolyA$ cutadapt --discard-trimmed --poly-a -j 20 -o NoPolyA/file.fastq file.fastq

I'm struggling to find any other tool that can do this

[marcelm]

You could try discarding all reads shorter than 50 bp using --minimum-length=50. That should get rid of all poly-A-trimmed reads.

[NickNCL]

That's a good idea, thanks