search

Daniel-Liu-c0deb0t / UMICollapse

Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.
MIT License
62 stars 8 forks source link

feature request: option to look for UMI in sam tag #13

Open eboyden opened 2 years ago

eboyden commented 2 years ago

Hi,

I'm investigating this software as a faster alternative to umi-tools, but our pipeline already extracts UMIs into the RX sam tag. Umi-tools can handle this with --extract-umi-method tag --umi-tag RX but it doesn't seem like UMICollapse has a similar option - would it be possible to add it?

Thanks!

Daniel-Liu-c0deb0t commented 2 years ago

Hey, this is a good suggestion. For now, a potential workaround is to write a simple script that extracts the RX tag and puts it at the end of the SAM record headers.