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innate2adaptive / Decombinator

Decombinator v4: fast, error-correcting analysis of TCR repertoires
https://innate2adaptive.github.io/Decombinator/
MIT License
22 stars 8 forks source link

No extended mouse tags, and no gamma/delta translate files #2

Open JamieHeather opened 7 years ago

JamieHeather commented 7 years ago

Currently mouse analysis lacks the resolution of the human as the original tag set only has IMGT-designated functional genes in it. There are certainly people using Decombinator on mouse data, it would be good to get this (and associated translation) up and running.

We also cannot translate gamma or delta repertoires (although as we aren't generating them for use with DCR to our knowledge this is a lower priority issue).

JamieHeather commented 7 years ago

Work is proceeding for extended mouse tags, which are relatively straightforward for TRBV, TRBJ and TRAJ genes. However, due to rampant duplications in the murine TRAV locus it is effectively impossible to distinguish between large numbers of different alpha V genes without complete transcript sequencing.

MVCowley commented 4 months ago

Looking at this issue again while updating the human tags.