Comments (8)
Hi Barbara,
Thanks for your query. Do you have paired (alpha/beta) data or just single chain?
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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
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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...
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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
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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?
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Ah sorry, I mean that I have only the CDR3 and they are roughly between 25000 and 50000 unique ones.
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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!
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Yes, I was already thinking about proceeding in this way, many thanks for your replies.
Barbara
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Related Issues (20)
- Feature request: save PCs from kPCA to log HOT 1
- Track the clonality of out of frame CDR3s HOT 2
- Limitations in detecting out of frame TCRs HOT 3
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- Validation Data Missing Epitope Label HOT 2
- Amino Acid sequence inputs HOT 7
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- AssertionError HOT 4
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- make_really_tall_trees.py script always running HOT 1
- text format cluster output for make_tall_trees.py HOT 2
- make_10x_clones_file.py issue HOT 2
- Bad CPU type HOT 4
- setup_gammadelta_db.py issue HOT 2
- usage with mixcr files HOT 8
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- Losing Clones
- Apply tcr-dist on amino acid sequences HOT 1
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