CellRanger 2.1.1

Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.

Accessing the software

To load the module:

module load CellRanger/2.1.1

The command source ${CELLRANGER_BASH} runs the Cell Ranger configuration file in the same bash shell.

An example command to include in your job script:

cellranger count [OPTIONS]

where [OPTIONS] is replaced with suitable input for the Cell Ranger tools.

Please note that some of the CellRanger pipelines (e.g. cellranger mkfastq) require the use of another module, bcl2fastq. To load this module, please execute:
module load bcl2fastq2/2.20.0-iomkl-2018a-Python-2.7.14

The Cell Ranger reference data sets and these are available in ${BB_APPS_DATA}/CellRanger/

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the website for more information regarding this application.

Last modified: 20 March 2019