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10x Genomics
Visium Spatial Gene Expression

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

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

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 \
Running preflight checks (please wait)...
- 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:

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:

Output Description
web_summary.html Data summary with images, metrics, and plots that can be used for quality assessment as well as errors and warnings related to data quality
metrics_summary.csv Metrics for quality assessment
cloupe.cloupe Loupe Browser file for data visualization and analysis
analysis/ Secondary analysis results (clustering, DGE, Moran's I)
spatial/ Folder containing Visium-specific outs: QC images to check image processing pipeline, downsampled input images, and files that describe spot barcode locations in the images
molecule_info.h5 Molecule level information used in additional pipelines
(spaceranger aggr, spaceranger targeted-compare)
Barcoded BAM (optional) Read alignment files
Filtered GEX Matrix Feature barcode matrices that contains only tissue-associated barcodes and are used in secondary analysis in R/Python
MEX: filtered_feature_bc_matrix/
HD5F: filtered_feature_bc_matrix.h5
Unfiltered GEX Matrix Feature barcode matrices that contains both tissue-associated as well as background barcodes and are used in secondary analysis in R/Python
MEX: raw_feature_bc_matrix/
HD5F: raw_feature_bc_matrix.h5

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:

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.