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marcelm / cutadapt

Cutadapt removes adapter sequences from sequencing reads
https://cutadapt.readthedocs.io
MIT License
513 stars 129 forks source link

poly-A trimming for paired-end data - consider orientation #753

Open benemead opened 8 months ago

benemead commented 8 months ago

Thanks @marcelm for maintaining such a useful tool!

Regarding the relatively new poly-A trimming feature - would it be possible to toggle strandedness?

By default you consider R1 to have the polyA and R2 to have polyT but for applications such as single cell RNA-seq, it can often be the opposite.

marcelm commented 8 months ago

Thanks for the feedback!

As a workaround, you can swap the R1 and R2 input and output files and the read-specific options (such as -a ↔ -A and -m ↔ -M).

This workoraund gets confusing quickly, so I will definitely think about how to make this configurable.

benemead commented 8 months ago

yep, that's what I've been doing 👍