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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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UMI dedup #512

Open zoeward-nz opened 1 year ago

zoeward-nz commented 1 year ago

Please can you specify how to use the dedup parameter WITH UMIs to dedup using the UMI information?

Also, am I able to use fastp --umi if the UMI is in a seperate file (as with Illumina bcl2fastq conversion)

Caffenicotiak commented 1 year ago

That would be indeed helpful. I think, the standard is to do this point later after mapping the reads but having it at an earlier point would allow to become aware of any problems with increased duplicates before doing most of the computationally intense parts.