A set of analysis piplines that perform sample demultiplexing, barcode processing, and single cell 3' gene counting.

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For detailed information, visit the Cell Ranger website.

Available Versions

To find the available versions and learn how to load them, run:

module spider cellranger

The output of the command shows the available Cell Ranger module versions.

For detailed information about a particular Cell Ranger module, including how to load the module, run the module spider command with the module’s full version label. For example:

module spider cellranger/5.0.0
ModuleVersion Module Load Command
cellranger5.0.0 module load cellranger/5.0.0
cellranger6.0.1 module load cellranger/6.0.1
cellranger7.0.1 module load cellranger/7.0.1
cellranger7.1.0 module load cellranger/7.1.0
cellranger7.2.0 module load cellranger/7.2.0

Important note on mkfastq

If you are using the mkfastq subcommand, please do not load the bcl2fastq2 module. Cell Ranger requires a statically linked binary of bcl2fastq, whereas the bcl2fastq2 module provides a dynamically linked binary. We have prepared a separate statically linked bcl2fastq, which will be made available to you automatically upon loading the cellranger module.