Track Clonotypes with TCR Sequence on standard Single Cell data (not scTCR-Seq)

Question

[Evan]

Hello,

I used MIXCR on standard Single Cell data and found some common clonotypes among my multiple conditions. I would like to know if it would be possible to track clonotypes with the TCR Sequence ? If yes, how ? I imagined I will have to search the TCR Sequence in the raw fastq file to identify to which cell it belongs with UMI Tools (I have fastq reads for each clonotype thanks to MIXCR) but I suppose there will be easier way to do that. The ultimate goal is to subset the clonotypes among my cells in Seurat and compare their expression between the different conditions.

Someone already tested something like that?

Thanks :)

Answer 1

[mizraelson]

Hi, what single cell protocol do you use? currently MiXCR series 4 supports single cell analysis for various platforms (10x, bd rhapsody etc). It is also possible to create a preset for any custom protocol.

More about supported kits here: https://docs.milaboratories.com/mixcr/reference/overview-built-in-presets/

In other words you can use MiXCR to directly identify clonotypes for every cell, you dont really need anything else.

If you have any questions on how to use the new MiXCR 4 or if you need help with your custom sc protocol please feel free to right us: https://github.com/milaboratory/mixcr or [e-mail]