scrnaseq
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Add TRUST4 for VDJ calling
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?
Also found WAT3R, which specializes on reconstructing from 10x 3' sequencing: https://github.com/mainciburu/WAT3R