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kmayerb / tcrdist3

flexible CDR based distance metrics
MIT License
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Lost Clones #90

Open TheRaspberryFox opened 1 year ago

TheRaspberryFox commented 1 year ago

Hello,

In TCRdist3, it seems that I am losing most of my clones (Single-cell paired 10X). I have around 4000 clones, but after running TCRdist3, I only have around ~200. The reason for the loss of these clones seems to be due to not matching the clones in this file: https://github.com/kmayerb/tcrdist3/blob/master/tcrdist/db/alphabeta_gammadelta_db.tsv. I noticed my data lacks some information required to match. Specifically, I lack the 01, 02, *03 identification at the end of the TRA and TRB genes.

I am thus interested in learning if there is good way to proceed that allows me to use the data I do have?

Thanks

kmayerb commented 1 year ago

The solution is to add *01 to your gene names.

On Mon, Aug 14, 2023 at 9:30 AM TheRaspberryFox @.***> wrote:

Hello,

In TCRdist3, it seems that I am losing most of my clones (Single-cell paired 10X). I have around 4000 clones, but after running TCRdist3, I only have around ~200. The reason for the loss of these clones seems to be due to not matching the clones in this file: https://github.com/kmayerb/tcrdist3/blob/master/tcrdist/db/alphabeta_gammadelta_db.tsv. I noticed my data lacks some information required to match. Specifically, I lack the 01, 02, *03 identification at the end of the TRA and TRB genes.

I am thus interested in learning if there is good way to proceed that allows me to use the data I do have?

Thanks

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