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 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 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: At this time, we do not have a pipeline for easily combining TCR or BCR data from 2 or more samples. For a pairwise comparison of 2 or more datasets, you can use the comparison mode in Loupe V(D)J Browser. Another work-around to combine 1 or more samples is by manipulating one of the input files for "cellranger vdj" pipeline called MRO file. This workaround is deprecated in Cell Ranger 4.0. Please use Cell Ranger v3.1, if you are interested in combining data using this method.