Jump to navigation Jump to search


cellranger website  

Cell Ranger is a set of analysis pipelines that processes Chromium single cell 3 RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. Cell Ranger 1.2 supports libraries generated by the Chromium Single Cell 3' v1 and v2 reagent kits.

Environment Modules

Run module spider cellranger to find out what environment modules are available for this application.

System Variables

  • HPC_CELLRANGER_DIR - installation directory
  • HPC_CELLRANGER_REF - reference data directory

Additional Information

Reference datasets can be found in the directory accessible via $HPC_CELLRANGER_REF variable.