Question: I have single-cell gene expression samples prepared with a cell hashing protocol. Can I use Cell Ranger to analyze these data?
Answer: 10x Genomics now supports Feature Barcoding technology for Cell Multiplexing (CellPlex). This technology utilizes species-agnostic, lipid-based tagging compatible with cells or nuclei to load up to 12 samples onto one GEM well. Please see this page for more information. We also provide the cellranger multi pipeline in Cell Ranger (6.0 or later) to analyze 10x Genomics Cell Multiplexing data.
If you have used custom antibody-based hashtag oligos (HTOs) for sample multiplexing, you may use the cellranger multi pipeline in Cell Ranger v6+ by providing a reference for custom multiplexing oligos. However, because the data generated from a custom workflow for multiplexing (e.g. CITE-seq) has not been validated with Cell Ranger’s algorithms, we cannot support custom workflows for multiplexing. Cell Ranger multi-web summaries will also provide a warning to customers to let them know a custom multiplexing reagent has been detected. Users should exercise caution when interpreting results generated with custom reagents.
If you encounter issues generating HTO libraries or any other custom reagents, we recommend contacting the vendor (e.g. New York Genome Center or BioLegend) directly.
Related article: How to analyze 5' multiplexed GEX+VDJ+FB(custom) data on multiple samples