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Choosing a Pipeline

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.
Future releases of Cell Ranger will not support 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.

  • 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 or BCL Convert 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.

Documentation by library typeCell Ranger pipeline
3' Gene Expressioncount
3' Gene Expression + Antibody/CRISPR Guide Capturecount
Antibody Capture onlycount
3' Gene Expression + Cell Multiplexing (+ Antibody/CRISPR Guide Capture)multi
Fixed RNA Profiling Gene Expression (+ Antibody Capture)multi
5' V(D)J onlyvdj
5' Gene Expression onlycount
5' Antibody Capture ± Gene Expressioncount
5' CRISPR (FB) + Gene Expressioncount
5' Gene Expression + V(D)J ± FBmulti
5' Gene Expression + V(D)J + Antigen Capture (BEAM) ± Antibody Capturemulti

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

  • Conduct secondary analysis to:

  • Find guidance and tips for troubleshooting failed Cell Ranger runs.