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wdecoster / chopper

MIT License
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Help with --contam parameter #25

Closed NikoLichi closed 6 months ago

NikoLichi commented 6 months ago

Hi there,

I have some scRNA-seq ONT fastq files that were generated following the FLAMES protocol. When checking for potential contaminants, several Illumina universal adapters exist, and I wonder if chopper could be used to trim those sequences. I saw the --contam parameter and wonder if this could be achieved like this(?)

I am aware of other Illumina trimming software like Trimmomatic, but don't know if this would be suitable for long-read data.

Thanks and all the best, Nicolas

wdecoster commented 6 months ago

That is not something that chopper can currently do. I wonder why you would want to remove those though, as an aligner will softclip those without problems.