10x Genomics
Visium Spatial Gene Expression

Space Ranger2.0, printed on 12/26/2024

Understanding Outputs

This page provides an overview of Space Ranger outputs for various supported workflows with links to detailed documentation for each of them.

Table of Contents

• Overview of output structure
• Space Ranger output files summary
  • Primary analysis: spaceranger count
  • Outputs for supported libraries of spaceranger count
  • Additional analysis: spaceranger aggr

Overview of output structure

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, spaceranger aggr, spaceranger targeted-compare 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:

$ 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 output files summary

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

Primary analysis: spaceranger count

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

Outputs for supported libraries of spaceranger count

The spaceranger count pipeline for Gene Expression, and Targeted Gene Expression analysis will output each of the types of files listed above. There are additional output files for CytAssist enabled Gene Expression, and Targeted Gene Expression libraries. For specific analysis output descriptions, select the library type below to go to the associated output documentation pages:

• CytAssist enabled Spatial Gene Expression: Spatial folder + Web Summary file
• Targeted Gene Expression: Targeted GEX Outputs
  • Additional analysis: Targeted-Compare outputs

Additional analysis: spaceranger aggr

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