10x Genomics
Chromium Single Cell Gene Expression

Cell Ranger6.1, printed on 11/05/2024

Choosing a Cell Ranger Pipeline

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.

• Start by choosing a computing option to set up and run Cell Ranger.
• Cell Ranger primary analysis pipelines require FASTQ files. If needed, convert raw sequence BCL files to FASTQ format with cellranger mkfastq (alternatively, use bcl2fastq from Illumina).
• Conduct primary analysis:
  
  • The table below shows the current recommendations for which pipeline to use for each library combination. Click on the library or combination of library types to go to the appropriate documentation.
  • Depending on the pipeline, go to these pages for help specifying FASTQ files for cellranger count or cellranger multi.

• Conduct secondary analysis to:
  • Aggregate datasets with cellranger aggr.
  • Reanalyze data using tunable parameters with cellranger reanalyze (currently not supported for Feature Barcode datasets).
  • Compare Targeted Gene Expression libraries with cellranger targeted-compare and evaluate sequencing depth with cellranger targeted-depth.
• Find guidance and tips for troubleshooting failed Cell Ranger runs.