Question: Can I aggregate data from Single Cell 3' libraries from v1 and v2 kits?
Answer: We do not support combining datasets from v1 and v2 kits using
cellranger aggr. The library structures are different and the v2 chemistry has increased sensitivity in terms of the number of genes and UMIs detected.
Some customers have merged v1 and v2 datasets and corrected for the batch effects using Seurat. Note: Seurat is a third-party software product. We are not staffed to answer questions about it or provide support for modifications.