CellRanger 5.0.1
There is a newer version of 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.Accessing CellRanger 5.0.1
To load the module for CellRanger 5.0.1 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):
module load CellRanger/5.0.1
BEAR Apps Version
Architectures
EL8-cascadelake — EL8-haswell — Ubuntu20.04-haswell
The listed architectures consist of two part: OS-CPU.
- BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
- BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.
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.
Other 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.
Last modified on 16th December 2020