Question: I have single cell gene expression samples prepared with a cell hashing protocol. Can I use Cell Ranger to analyze these data?
Answer: Please note that 10x Genomics does not currently offer a commercialized kit that supports cell hashing.
However, if you have used antibody-based hashtag oligos (HTOs) for multiplexing samples, Cell Ranger may be used to produce UMI counts for the HTOs, similar to other types of Feature Barcoding data analysis. You will then need custom scripts or third-party tools (for example Seurat) to further process the data, such as multiplet detection, demultiplexing hashed samples, etc.
As 10x Genomics has not developed or validated workflows utilizing HTO tags for cell hashing, we can only provide limited support with respect to troubleshooting the workflow. However, if you encounter issues generating HTO libraries, we recommend contacting New York Genome Center or BioLegend directly.