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phbradley / tcr-dist

Software tools for the analysis of epitope-specific T cell receptor (TCR) repertoires (scroll down for the README)
MIT License
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Estimation of TCRdiv #39

Closed bravib closed 4 years ago

bravib commented 4 years ago

Good evening, after reading your paper I would be interested in estimating TCRdiv of a series of epitope-specific repertoires, however I do not find a script dedicated only to it without the need of running the full analysis. Could you please help me with this? Does one need also the alpha-chain to estimate TCRdiv? Many thanks, best regards, Barbara

phbradley commented 4 years ago

Hi Barbara, Thanks for your query. Do you have paired (alpha/beta) data or just single chain?

bravib commented 4 years ago

I actually have only beta chains, so I was wondering if the TCRdiv measure is applicable, limiting the evaluation of the distance to these chains. Many thanks, Barbara

phbradley commented 4 years ago

OK, one more question-- roughly how big are your repertoires? Hundreds, thousands, millions? I also have a C++ repository that can compute TCRdiv and scale to larger datasets...

bravib commented 4 years ago

I see, in terms of unique sequences they are between 25000 and 50000 and I look at the CDR3 region (while I know that TCRdist is calibrated not only on the CDR3). Thanks a lot for your help, Barbara

phbradley commented 4 years ago

OK, and do you only have the CDR3 or do you mean that when you look only at the CDR3 you have 25000 to 50000 unique sequences?

bravib commented 4 years ago

Ah sorry, I mean that I have only the CDR3 and they are roughly between 25000 and 50000 unique ones.

phbradley commented 4 years ago

Hi Barbara, without the V genes it's not really possible to compute TCRdist. You could try something like a simple Hamming distance or Levenshtein distance on the CDR3s and try using the same formula for TCRdiv, but I don't have code to help with that. Sorry!

bravib commented 4 years ago

Yes, I was already thinking about proceeding in this way, many thanks for your replies. Barbara