Skip to content

Space Ranger Count Specifications

Process Details

  • Name: Space Ranger Count
  • Process UUID: f931nsen1cyqe8bn0sgipekals0ivj
  • Process Group: Spatial

Overview

This process runs 10x Genomics' Space Ranger on the reads and images, performing spatial gene expression analysis by aligning reads to the reference genome. The process analyzes spatial transcriptomics data by processing FASTQ files alongside histology images to generate spatially-resolved gene expression profiles.

This process is implemented in Bash, which orchestrates the Space Ranger pipeline for spatial gene expression quantification.

Key Functionality

  • Spatial Gene Expression Analysis: Aligns sequencing reads to a reference genome while maintaining spatial coordinate information from tissue sections
  • Image Processing: Processes both CytAssist and microscope brightfield images to enable spatial mapping of gene expression
  • Data Integration: Combines sequencing data with histological images to create spatially-resolved expression matrices

Input/Output Specification

Inputs

Required Inputs

  • Reference Genome Archive

    • Description: Compressed reference genome and annotation files for read alignment
    • Format: tar.gz

  • Sample Sheet

    • Description: Metadata file containing sample information and experimental parameters
    • Format: Samplesheet

  • Input Configuration File

    • Description: Tab-separated file specifying input file paths and processing parameters
    • Format: TSV

Outputs

  • Space Ranger Output Archive

    • Description: Complete Space Ranger analysis results including gene expression matrices, spatial coordinates, and quality control metrics
    • Format: tar.gz (set)

  • Processed Tissue Image

    • Description: Processed brightfield microscopy image used for spatial mapping, formatted for downstream visualization
    • Format: TIF

References & Resources

  • Tool Documentation: 10x Genomics Space Ranger Official Documentation (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger)
  • 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