Question: I have data generated with 5' v1.1 chemistry. Can I combine it with data generated using 5' v2 chemistry?
Answer: Yes, you can combine 5’ v1 chemistry data with 5’ v2 chemistry data. Here are some considerations based on the library type:
- Gene expression data: For combining gene expression libraries, use
cellranger aggrwith chemistry correction. Refer to this article for more information on when to use chemistry correction.
- Cell surface protein data: For combining cell surface protein and dCODE™ Dextramer® data, use
cellranger aggr. The chemistry correction option has not been validated for cell surface protein and dCODE™ Dextramer® libraries. Therefore, we do not recommend using chemistry correction when combining these library types.
- Gene expression with cell surface protein data: Use
cellranger aggrwith chemistry correction. The pipeline uses chemistry correction for combining gene expression data, whereas the cell surface protein data are combined without any correction.
- TCR and BCR data: Starting from Cell Ranger version 5.0, it is possible to aggregate multiple V(D)J libraries through the
cellranger aggrpipeline. For more information, please refer to our support page and additional article.
Note: It is recommended to have the same Cell Ranger version for
count/multiruns before aggregating.
Products: Single Cell Immune Profiling