Question: I have pooled multiplex samples in my 5'GEX and TCR/BCR libraries using TotalSeqC or other custom methods. Can I use Cell Ranger to analyze the data and generate outputs for each sample separately?
Answer:
| Update: Cell Ranger versions 9.0+, have streamlined the analysis of multiplexed cells and samples using antibody hashtags (also known as cell or sample hashing). You no longer need to use the workarounds documented in this article. We recommend using Cell Ranger 9.0+ to analyze your cell-hashed data. Please see here for more guidance on how to run the pipeline. |
If you have 5' cell multiplexed libraries and need to analyze the data, you can use the process outlined here. Please note that you will need to use Cell Ranger v9.0+. Please also note that cell multiplexing for 5' Immune Profiling libraries is currently not supported by 10x.
However, we do provide unofficial workaround for 5' Immune Profiling multiplexed libraries. Please refer to our latest resources linked below:
- Analysis Guide Tutorial: Demultiplexing and Analyzing 5' Immune Profiling Libraries Pooled with Hashtags
- Public Dataset: Demultiplexing 5' Immune Profiling Libraries Pooled with Hashtags
- Q&A Article: Can I perform Cell Hashing in the 5' Single Cell Immune Profiling Workflow?
Note: If your 5’ cell multiplexing data is generated using 10x single cell HT kits, please use Cell Ranger version 7 or above for data analysis. In the chemistry field of the web summary HTML file, "HT" will be indicated if the cell multiplexing data is generated with HT kits. If Cell Ranger fails to detect HT for your 5’ HT cell multiplexing data, please specify SC5PHT for the ‘chemistry’ option in the multi config csv file and re-run Cell Ranger.
Products: Single Cell Immune Profiling
Last updated: Oct 2023