Skip to content

Space Ranger Adapter Specifications

Process Details

  • Name: space_ranger_adapter
  • Process UUID: c663t01kuuq8ow2pzk7prlbtme5b92
  • Process Group: Spatial

Overview

This process serves as an adapter for exposing select Space Ranger count outputs from 10x Genomics spatial transcriptomics analysis. It extracts and organizes key output files from compressed Space Ranger results, making them accessible for downstream spatial analysis workflows. The process specifically handles Visium HD data with support for both standard 8μm and high-resolution 2μm spatial resolutions.

This process is implemented in Bash, which extracts and reorganizes Space Ranger output files using standard Unix utilities.

Key Functionality

  • Output Extraction: Extracts compressed Space Ranger results and organizes files into accessible formats
  • Multi-Resolution Support: Handles both standard 8μm resolution and high-resolution 2μm spatial data for Visium HD experiments
  • File Format Conversion: Prepares various output formats including H5 matrices, HTML reports, and Loupe Browser files
  • Spatial Data Organization: Structures spatial imaging data and associated metadata for downstream analysis

Input/Output Specification

Inputs

Required Inputs

  • Space Ranger Output Archive
    • Description: Compressed tar.gz archive containing complete Space Ranger count analysis results
    • Format: tar.gz

Outputs

  • Cloupe File

    • Description: Loupe Browser file for interactive visualization of 8μm resolution spatial data
    • Format: cloupe

  • H5 Matrix Files

    • Description: Multiple H5 files including filtered and raw feature-barcode matrices, molecule info, and feature slice data for high-resolution analysis
    • Format: h5

  • Web Summary Report

    • Description: HTML report containing analysis metrics, quality control plots, and spatial visualization
    • Format: html

  • Metrics Summary

    • Description: Tab-separated file containing key analysis metrics and statistics
    • Format: tsv

  • Spatial Data Directory

    • Description: Directory containing spatial imaging data, tissue positions, and associated metadata files
    • Format: directory

References & Resources

  • Tool Documentation: Contact the team for details on Space Ranger analysis pipeline
  • Related Papers: Ståhl, P.L., Salmén, F., Vickovic, S. et al. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science 353, 78-82 (2016). DOI: 10.1126/science.aaf2403