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

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

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

Copy
cd /home/jdoe/runs spaceranger count --id=sample345 \
                --fastqs=/home/jdoe/runs/HAWT7ADXX/outs/fastq_path \
                --transcriptome=/opt/refdata-gex-GRCh38-2020-A \
                --image=/home/jdoe/runs/image.tif \
                --slide=V19J01-123 \
                --area=B1


Running preflight checks (please wait)...

Outputs:
- Run summary HTML:                 /home/jdoe/runs/sample345/outs/web_summary.html
- Outputs of spatial pipeline:
    aligned_fiducials:              /home/jdoe/runs/sample345/outs/spatial/aligned_fiducials.jpg
    detected_tissue_image:          /home/jdoe/runs/sample345/outs/spatial/detected_tissue_image.jpg
    scalefactors_json:              /home/jdoe/runs/sample345/outs/spatial/scalefactors_json.json
    tissue_hires_image:             /home/jdoe/runs/sample345/outs/spatial/tissue_hires_image.png
    tissue_lowres_image:            /home/jdoe/runs/sample345/outs/spatial/tissue_lowres_image.png
    cytassist_image:                null
    aligned_tissue_image:           null
    tissue_positions:               /home/jdoe/runs/sample345/outs/spatial/tissue_positions.csv
    spatial_enrichment:             /home/jdoe/runs/sample345/outs/spatial/spatial_enrichment.csv
    barcode_fluorescence_intensity: null
- Run summary CSV:                                           /home/jdoe/runs/sample345/outs/metrics_summary.csv
- Correlation values between isotypes and Antibody features: null
- BAM:                                                       /home/jdoe/runs/sample345/outs/possorted_genome_bam.bam
- BAM BAI index:                                             /home/jdoe/runs/sample345/outs/possorted_genome_bam.bam.bai
- BAM CSI index:                                             null
- 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
- 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
- Feature Reference:                                         null
- Target Panel file:                                         null
- Probe Set file:                                            null
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
• /home/jdoe/runs/sample345/outs/ contains the final pipeline output files

More information about the contents of the pipeline output directory can be found in the Pipestance Structure page.

Space Ranger maintains 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. Visium-specific data, including spot and molecular barcodes, can be accessed using any third-party tools or scripts that can parse the additional elements utilized by Space Ranger.

The outputs generated from the primary analysis pipeline spaceranger count for Gene Expression (GEX) contained in the outs/ directory are summarized below:

The spaceranger count pipeline for Gene Expression and Protein Expression analysis will output each of the types of files listed above. There are additional output files for Visium CytAssist-enabled Gene Expression and Protein Expression libraries. For specific analysis output descriptions, see this page.

The spaceranger aggr pipeline outputs metrics, web summary, filtered feature-barcode matrices, and a .cloupe file within the outs/ directory. Refer to the aggr outputs page for more details.

Space Ranger v2.1 supports protein expression analysis with built-in isotype normalization to correct for technical noise that is inherent in antibody-based assays. The filtered feature barcode matrices contain the normalized counts while the raw feature barcode matrices contain raw UMI counts. For convenience, the normalization factor is provided in the outputs.

The isotype_normalization_factors.csv has the following columns: