Hi,

I'm working on TCR data from RNA (not scRNA) but MiXCR did a great job on identifying VDJ regions and VDJtools works well for R plotting.

Hope this helps and would love to learn along with this question.

MiXCR: https://mixcr.readthedocs.io/en/master/index.html

VDJtools: https://vdjtools-doc.readthedocs.io/en/master/

I think you could try this:

doi: 10.1038/s41592-021-01142-2. Epub 2021 May 13.. 2021 Jun;18(6):627-630.Nat Methods

TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data

Li Song 1 2, David Cohen 1, Zhangyi Ouyang 3, Yang Cao 4, Xihao Hu 1 2, X Shirley Liu 5 6 7

Affiliations expand

• PMID: 33986545
• PMCID: PMC9328942
• DOI: 10.1038/s41592-021-01142-2