How can I combine and compare data from 5’v1/v1.1 chemistry with 5’v2 chemistry?

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 aggr with 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 aggr with 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 aggr pipeline. For more information, please refer to our support page and additional article. 

Note: The above applies to integrate data with 5'v3 chemistry as well. It is recommended to have the same Cell Ranger version for count/multiruns before aggregating.

Related Article: Can I aggregate gene expression data from different chemistries ? 

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