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Add TRUST4 for VDJ calling

Open grst opened this issue 3 years ago • 1 comments

Is your feature request related to a problem? Please describe

TRUST4 claims they can call TCRs not only from VDJ-enriched 10x data, but also regular 10x 5' seq and other scRNA-seq protocols. Since that enables TCR analysis to a lot of datasets where this was not previously possible, I believe this would be a nice addition.

More details about TRUST4:

  • https://github.com/liulab-dfci/TRUST4
  • https://www.nature.com/articles/s41592-021-01142-2

Describe the solution you'd like

Run TRUST4 (enable explicitly, as not all datasets contain B or T cells) and create AIRR rearrangement output, and optionally a scirpy-compatible Anndata-file (related to #68)

Describe alternatives you've considered

Not sure if this is in scope of this pipeline, as not applicable to all datasets. Maybe also related to #bcellmagic?

grst avatar Oct 27 '21 18:10 grst

Also found WAT3R, which specializes on reconstructing from 10x 3' sequencing: https://github.com/mainciburu/WAT3R

grst avatar Mar 02 '22 14:03 grst