Cell Ranger provides a set of analysis pipelines that process single cell data from 10x Genomics Chromium instruments 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 pipelines for primary analysis:
cellranger multi(recommended)cellranger countcellranger vdj
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 support@10xgenomics.com