An overview of Cell Ranger outputs for different pipelines and products is described below, with links to detailed documentation for each section.

All pipelines produce all of their output in a single pipeline output directory, whose name depends on the pipeline

• For cellranger mkfastq, the --id argument is used, or if unspecified, the flow cell ID is used (e.g., HAWT7ADXX).

• For Cell Ranger count, multi, vdj, aggr, and reanalyze, the --id argument is used.

Output files will appear in the outs/ subdirectory within this pipeline output directory. For example, a typical cellranger count analysis may display the following after completion:

Copy
cd /home/jdoe/runs
cellranger count --id=sample345 \
                --transcriptome=/opt/refdata-gex-GRCh38-2020-A \
                --fastqs=/home/jdoe/runs/HAWT7ADXX/outs/fastq_path \
                --indices=SI-3A-A1

Martian Runtime - v4.0.8

Running preflight checks (please wait)...
2016-01-01 10:23:52 [runtime] (ready)           ID.sample345.CELLRANGER_CS.CELLRANGER.SETUP_CHUNKS
...

2012-01-01 12:10:09 [runtime] (join_complete)   ID.sample345.CELLRANGER_CS.CELLRANGER.SUMMARIZE_REPORTS

Outputs:
- Run summary HTML:                      /home/jdoe/runs/sample345/outs/web_summary.html
- Run summary CSV:                       /home/jdoe/runs/sample345/outs/metrics_summary.csv
- BAM:                                   /home/jdoe/runs/sample345/outs/possorted_genome_bam.bam
- BAM index:                             /home/jdoe/runs/sample345/outs/possorted_genome_bam.bam.bai
- Filtered feature-barcode matrices MEX:    /home/jdoe/runs/sample345/outs/filtered_feature_bc_matrix
- Filtered feature-barcode matrices HDF5:   /home/jdoe/runs/sample345/outs/filtered_feature_bc_matrix.h5
- Unfiltered feature-barcode matrices MEX:  /home/jdoe/runs/sample345/outs/raw_feature_bc_matrix
- Unfiltered feature-barcode matrices HDF5: /home/jdoe/runs/sample345/outs/raw_feature_bc_matrix_h5.h5
- Secondary analysis output CSV:         /home/jdoe/runs/sample345/outs/analysis
- Per-molecule read information:         /home/jdoe/runs/sample345/outs/molecule_info.h5
- Loupe Browser file:               /home/jdoe/runs/sample345/outs/cloupe.cloupe

Pipestance completed successfully!

In this case,

• /home/jdoe/runs/ is where the pipeline was run,
• /home/jdoe/runs/sample345/ is the top-level output directory containing pipeline metadata, and
• /home/jdoe/runs/sample345/outs/ contains the final pipeline output files.

More information about the contents of the Cell Ranger pipeline output directory can be found in the Advanced section's Pipestance Structure page.

The Cell Ranger software strives to maintain compatibility with common analysis tools by using standard output file formats whenever possible. For example, the barcoded BAM files can be viewed in standard genome browsers such as IGV to verify alignment quality and other features. Data specific to 10x Genomics products, including cellular and molecular barcodes, can be accessed by third-party tools or scripts that can parse the additional elements utilized by Cell Ranger.

For primary analysis, the cellranger count, cellranger vdj, and cellranger multi pipelines will output the following types of files:

• web summary (HTML) (count, multi, vdj)
• metrics summary CSV
• BAM
• raw and filtered feature-barcode matrices (MEX, H5)
• secondary analysis files (CSV)
• molecule info (H5)
• Loupe files (cloupe and vloupe)

Cell Ranger computes application results metrics for each supported library type. Supported library types are "Gene Expression" for standard gene expression data, and the Feature Barcode-specific library types "Antibody Capture", "CRISPR Guide Capture", "Cell Multiplexing", and "Custom" (user-defined assays that are neither Antibody nor CRISPR). Feature Barcode metrics will be computed and displayed only when one of these library types was used in the assay. Metric descriptions for each supported library are available.

Cell Ranger pipelines used for analyzing V(D)J data (multi and vdj) will output additional files, described in:

• VDJ-T/B analysis with cellranger vdj
• VDJ + GEX + BEAM analysis with cellranger multi

The cellranger count pipeline for Gene Expression, Antibody Capture, and CRISPR Guide Capture, will each output the types of files listed above.

For specific analysis output descriptions, select the library type below to go to the associated outputs documentation pages:

The cellranger aggr pipeline will output a web summary, a filtered matrix, and a .cloupe file all within a directory called outs/. See aggr outputs section for more information.

The cellranger reanalyze pipeline will produce a secondary analysis web summary and a .cloupe file within a secondary analysis output directory called outs/. See the secondary analysis outputs page for details about reanalyzed outputs.