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OpenGene / fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
MIT License
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Dovetail (adapter) removal not working correctly #481

Open nchernia opened 1 year ago

nchernia commented 1 year ago

We have ATAC data that we want to remove the overlapping dovetails from; however, one read end is 150bp and the other is 50bp. Fastp is not doing trimming correctly in this scenario. There seems to be a hard cap at 50, so that the reads are trimmed from 31 to 50 but then nothing is trimmed to any length between 50 and 150, despite there still being overlaps in that section.

mehdiborji commented 2 months ago

Hi @nchernia I wonder if you could find a solution for such a problem. I have similar problem where reads lengths are asymmetric and fastp with default options fails to detect adapter in the longer read because it's not observed in the shorter read.