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innate2adaptive / Decombinator

Decombinator v4: fast, error-correcting analysis of TCR repertoires
https://innate2adaptive.github.io/Decombinator/
MIT License
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Using other species gene sets from IMGT #17

Open tprkp opened 4 years ago

tprkp commented 4 years ago

Hi,

Just wondering how difficult it would be to create tags for other species. I am currently using Repseqio to create libraries for MiXCR but want to do a comparison of analysis. Is there a pipeline to search for gene-unique tags?

Kind regards, Ting

JamieHeather commented 4 years ago

Hi Ting,

There are a few pipelines but they all still currently require a fair amount of manual handling, so they've not been uploaded yet. However it's potentially something that we could polish up and share if it'd be useful.

Either way I'd be happy to discuss the process. What species/loci were you thinking about?

Jamie

tprkp commented 4 years ago

Hi Jamie,

Thanks for getting back to me. I’m interested in the Common Marmoset (Callithrix Jacchus). There are sequences available on IMGT, but it may take some manipulation depending on what is needed as inputs as some of the entries are sparsely annotated.

Kind regards, Ting

JamieHeather commented 4 years ago

Effectively all we need as a starting point we need the DNA sequences for all the V and J genes for the loci you're interested in.

Hmm it's odd, I can find lots of mentions of Callithrix Jacchus being in IMGT, but no actual data - they don't seem to be an option in GENE-DB.

MVCowley commented 4 months ago

Working on a pipeline to generate a tag set from a species on IMGT at present.