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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 analysis with XT-HS library #401

Open lmanchon opened 2 years ago

lmanchon commented 2 years ago

Hello, I use the SSEL XT-HS/Low Input kit from Agilent and the UMIs are positioned at index 2 (see picture below Molecular_Barcode ). The UMIs are in a separate FASTQ file.

Is fastp able to handle this type of build and how do I set up the UMI file in the fastp command? Thank you.

LukaP-BB commented 2 years ago

Hi, to my knowledge fastp doesn't handle this case, thus I made a custom tool some time ago to generate fastqs with the UMIs in the headers, in the same fashion as fastp. This was developed for internal use so the documentation is minimal, but I'm available to help for troubleshooting if needed : https://gitlab.com/luka.pavageau/xths_umi_formatter

lmanchon commented 2 years ago

Hi, ok it seems to be good for my job. but is there a README file to compile the package ?

LukaP-BB commented 2 years ago

Hi, I updated the readme with install instructions and added a pre-compiled bin for linux in the repo.

lmanchon commented 2 years ago

ok thank you for your help