Contents
Cell Ranger
Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.
Note: At present, we are not providing References for any species. HPC users will have to download and build these as needed.
Usage
Cell Ranger has different pipelines intended for different experiments. It is recommended that HPC users read the Cell Ranger documentation, available here, for details on the available pipelines and the various command options before reading this section of our wiki.
The sections below describe how to run Cell Ranger on our HPC system.
Running Cell Ranger in an Interactive Session
To run Cell Ranger in an interactive session see same usage below
