Cell Ranger

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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.

Required Modules


  • cellranger

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.