10x Genomics CellRanger multi pipeline: 10x_multi_config[.SAMPLE].csv

For certain types of 10x Genomics data, the QC pipeline will automatically run the cellranger multi pipeline to perform appropriate analyses (for example, multiplexing analyses for CellPlex data), provided that:

  1. The cellranger_multi QC module is specified as part of the protocol, and

  2. one or more configuration files for running CellRanger multi are present in the analysis project directory.

The configuration files should be named either 10x_multi_config.csv (appropriate if there is a single physical sample in the dataset) or 10x_multi_config.<SAMPLE>.csv (the more general form when there is one or more physical sample, in which case <SAMPLE> should be a label for each physical sample in the dataset).

Note

Currently the physical sample name in the configuration file name is arbitrary and doesn’t have to match the sample names for the Fastq files.

A template version of the file (called 10x_multi_config.csv.template) is automatically generated and partially populated by the setup_analysis_dirs command for the appropriate single cell data type (see Processing 10x Genomics single cell data). The template file is ignored by the QC pipeline, so it must be manually copied, renamed and edited for each physical sample that the multi command should be run on.

Specifically, at a minimum:

  1. The physical sample name should be added into the file name (if there are multiple physical samples);

  2. The [libraries] section should be edited to remove any Fastqs associated with other physical samples, and the feature_types field for each Fastq ID should be updated to assign the correct feature type (e.g. Gene expression, Multiplexing capture etc;

  3. The samples section should be removed or edited as appropriate for the type of data being analysed (for example, assigning CMOs to multiplexed sample names for CellPlex dataset).

Any additional options (for example, forcing numbers of cells) can be included if required - details of the format of the multi configuration file for different applications can be found via the CellRanger documentation:

The QC pipeline will attempt to run cellranger multi for each of the appropriately named configuration files in the project directory. Currently this is supported for the following library types:

The following library types are explicitly (not yet) supported: