Cell Ranger v7.2 (and later) does not support Targeted Gene Expression analysis. Use Cell Ranger v7.1 to analyze your Targeted Gene Expression libraries.
Cell Ranger v7.2 is the last version to support the analysis of Low Throughput (LT) libraries.
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.
Cell Ranger has three analysis pipelines for primary analysis
cellranger countcellranger vdjcellranger multi
Input files required for each of these pipelines is described on the List of Inputs page.
Refer to the table below for 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
- 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]