10xGenomics CellPlex and Flex datasets: 10x_multi_config.csv

For 10xGenomics CellPlex (cell multiplexing) and Flex (fixed RNA profiling) data, multiplexing analyses are run using the cellranger multi command, provided that a 10x_multi_config.csv file is also present in the project directory.

Note

Template versions of this file will be automatically and partially populated by the setup_analysis_dirs command for the appropriate single cell data type (see Processing 10x Genomics single cell data).

Depending on the library type, this file should have the format and content outlined in the following 10x Genomics documentation:

• CellPlex: cellranger_multi_cellplex

• Flex: cellranger_multi_frp

• Single cell immune profiling: `cellranger_multi