Cell Ranger provides a set of analysis pipelines that process Chromium Single Cell Gene Expression data to align reads, generate Feature Barcode matrices, perform clustering and other secondary analysis, and more.
Find your primary pipeline and learn how to use it
Select your library type(s) above, and we will guide you to the appropriate pipeline and corresponding documentation.
Cell Ranger has three analysis pipelines for primary analysis
cellranger countcellranger vdjcellranger multi
The required input files for each of these pipelines are described on the List of Inputs page.
Refer to the table below to find the recommended pipeline for each library combination. Click on the library type for detailed documentation and FASTQ file specifications.
Conduct secondary analysis to:
- Aggregate datasets with cellranger aggr
- Generate automated cell type annotations with cellranger annotate
- Reanalyze data using tunable parameters with cellranger reanalyze (currently not supported for Feature Barcode datasets)
- Find guidance and tips for troubleshooting failed Cell Ranger runs
- For assistance with a specific library combination not documented here, please contact [email protected]