UMI analysis with XT-HS library

[lmanchon]

Hello, I use the SSEL XT-HS/Low Input kit from Agilent and the UMIs are positioned at index 2 (see picture below ). 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]

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]

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

[LukaP-BB]

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

[lmanchon]

ok thank you for your help