Cell Ranger ATAC

Overview

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

Using

Use the module name cell-ranger-atac to discover versions available and to load the application.

Multicore

The cellranger-atac application is built with a number of sub commands. Run cellranger-atac -h to view what are available. View the particular sub command's help to view multi core options. For example cellranger-atac count -h

There are various --local<cores|mem|vmem> options that can be looked at - but from observations it appears the number of cores requested are the number of cores that cellranger-atac will pick up and use.

Cell Ranger ATAC can be run in a number of different ways:

1. Single Server: We do not have Cell Ranger ATAC running on a single server - any jobs will have to be submitted to the cluster using sbatch and/or run using salloc.

2. Job Submission Mode: “Cell Ranger ATAC can be run in job submission mode, by treating a single node from the cluster like a local server” This will run on a single compute node - you will either have to sbatch or job to the queue, or create an interactive session using salloc.

3. Cluster Mode: Please note that “10x Genomics does not officially support Slurm or Torque/PBS.“

Reference Data

The following reference data has been downloaded and unpacked in the following location: