Request for Assistance with 10x 5' V3 GEX Expression Data Processing in mixcr v4.7.0

[ytdai]

Dear MiLaboratories Support Team,

I hope you are doing well.

We are interested in identifying V(D)J sequences (especially TCR γ/δ) directly from 10x Genomics 5′ GEX data. In earlier versions of MiXCR, the mixcr analyze 10x-sc-5gex workflow provided a convenient way to recover immune receptor sequences from 10x Genomics 5′ data, which was very useful for our analyses.

Could you please let us know whether this functionality could be extended or updated to support 10x 5′ V3 GEX chemistry? This would be particularly valuable for γδ T cell studies, where dedicated V(D)J libraries often provide limited or suboptimal results.

Thank you very much for your time and support.

Best regards,
Yuting DAI

[zthoms]

This seems to work:

mixcr analyze 10x-sc-xcr-vdj
--species hsa
--tag-pattern "^(CELL:N{16})(UMI:N{12})^(R2:*)"
--set-whitelist CELL=file:3M-5pgex-jan-2023.txt # can get this from the cellranger directory
fastq_r1
fastq_r2
output

[mizraelson]

With the latest MiXCR version you can use:

mixcr analyze 10x-sc-5gex-gemx-v3
--species hsa
--tag-pattern "^(CELL:N{16})(UMI:N{12})^(R2:*)"
--set-whitelist CELL=file:3M-5pgex-jan-2023.txt # can get this from the cellranger directory
fastq_r1
fastq_r2
output