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. Please use the following considerations for each library type when combining and comparing the data.
Gene expression data: For combining gene expression libraries, you can use “cellranger aggr” with chemistry correction. Please see this article for more information on when to use chemistry correction.
Cell surface protein data: For combining cell surface protein and dextramer data, you can use
cellranger aggr. We have not validated the chemistry correction option for cell surface protein and dextramer libraries and therefore do not recommend using this option when combining these library types.
Gene expression with cell surface protein data: You can use
cellranger aggr with chemistry correction. The pipeline will use chemistry correction for combining gene expression data and the cell surface protein data will be 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 aggr pipeline. For more information, please refer to our support page and additional article.
Products: Single Cell Immune Profiling