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  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:

Code Block
/apps/u/opt/linux/cell-ranger-atac/
  refdata-cellranger-arc-GRCh38-2020-A-2.0.0
  refdata-cellranger-arc-mm10-2020-A-2.0.0
  refdata-cellranger-atac-GRCh38-and-mm10-2020-A-2.0.0