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.
module spider cellranger to find out what environment modules are available for this application.
- HPC_CELLRANGER_DIR - installation directory
- HPC_CELLRANGER_REF - reference data directory
Reference datasets can be found in the directory accessible via $HPC_CELLRANGER_REF variable.