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: If you have 5' cell multiplexed libraries and need to analyze the data, you may be able to use a workaround to enable the processing of cell multiplexed 5’ data with Cell Ranger. Please 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?