CellRanger-ATAC 2.0.0

Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.

Accessing CellRanger-ATAC 2.0.0

To load the module for CellRanger-ATAC 2.0.0 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load CellRanger-ATAC/2.0.0

BEAR Apps Version

2020a

Architectures

EL8-cascadelakeEL8-haswellUbuntu20.04-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 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-ATAC website.

Other Versions

These versions of CellRanger-ATAC 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
1.2.0 2020a

Last modified on 18th May 2021