CellRanger

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.

CellRanger Reference Data

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

CellRanger and bcl2fastq

Please note that some of the CellRanger pipelines (e.g. cellranger mkfastq) require the use of another application: bcl2fastq. If required, please select a version bcl2fastq2 to use.

More Information

For more information visit the CellRanger website.

Available Versions

These versions of CellRanger are available on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Version BEAR Apps Version
7.0.0 2021a
6.0.1 2020b
5.0.1 2020a
3.1.0 2019a
3.0.2 2018b