10x Genomics
Chromium Single Cell Immune Profiling

Cell Ranger6.1, printed on 12/03/2024

Choosing a Cell Ranger Pipeline

Cell Ranger provides a set of analysis pipelines for processing Chromium Next GEM Single Cell Immune Profiling data to align reads, generate Feature Barcode (FB) matrices, perform clustering and secondary analyses, and more.

• Start by choosing a computing option to set up and run Cell Ranger.

• Cell Ranger pipelines require FASTQ files. If needed, convert raw sequence BCL files to FASTQ format with cellranger mkfastq (alternatively, use bcl2fastq).

• 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.

For assistance with a specific library combination not documented here, please contact [email protected]

• 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.