Support UMI extraction - Githubissues

jdidion / atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

Other

120 stars 15 forks source link

Support UMI extraction #61

Closed jdidion closed 4 years ago

jdidion commented 6 years ago

Some library preparations add UMIs to one or both ends of the template sequence. This new feature will support:

[x] Removing UMIs of specified length from one or both reads in the pair.
[x] Adding the UMIs to the read header
[ ] Emitting the UMIs to one or a pair of FASTQ files in the same order as the reads.

jdidion commented 6 years ago

Thanks to @wckdouglas, this is now implemented in the develop branch!

chapmanb commented 6 years ago

Douglas and John; Wow, thanks so much for working on this. We currently use either umis (https://github.com/vals/umis) or fastp (https://github.com/OpenGene/fastp#unique-molecular-identifer-umi-processing) for this but it would be awesome to be able to trim, filter and UMI process all together with atropos as an option.

Would you be able to support an option to prefix the UMI, like the --umi_prefix option in fastp? That would help us be able to feed output for atropos UMI labeling into downstream tools like fgbio (https://github.com/fulcrumgenomics/fgbio).

Thanks again for working on this.

jdidion commented 6 years ago

Hi Brad, absolutely. Could you open a separate issue for this?

On Mar 18, 2018, at 12:11 PM, Brad Chapman notifications@github.com wrote:

Douglas and John; Wow, thanks so much for working on this. We currently use either umis (https://github.com/vals/umis) or fastp (https://github.com/OpenGene/fastp#unique-molecular-identifer-umi-processing) for this but it would be awesome to be able to trim, filter and UMI process all together with atropos as an option.

Would you be able to support an option to prefix the UMI, like the --umi_prefix option in fastp? That would help us be able to feed output for atropos UMI labeling into downstream tools like fgbio (https://github.com/fulcrumgenomics/fgbio).

Thanks again for working on this.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub, or mute the thread.

chapmanb commented 6 years ago

John -- thanks so much for this. I've been digging into this more and realized I can do this right now by setting --delim :UMI_. Apologies for missing this option on an initial read. I did have one more feature related to extracting the UMI from a separate read, and raised a separate issue for this. Thanks again for atropos and considering all these inputs.

jdidion commented 4 years ago

Right now I'm not going to implement the writing of separate output files with UMIs. If there is a compelling use case for this, please open a separate issue.