10x Genomics Support/Space Ranger 2.1/Analysis/

Choosing a pipeline

Space Ranger provides a set of analysis pipelines that allows for processing of Visium Spatial Gene Expression (GEX) and Protein Expression (PEX) data with brightfield and fluorescence images to align reads, generate Feature Barcode matrices, and perform secondary analysis including clustering and differential gene expression.

  • Start by choosing a computing option to set up and run Space Ranger.
  • Space Ranger requires FASTQ files as input. If you are starting with raw sequence BCL files, first demultiplex them to FASTQ using either spaceranger mkfastq or BCL Convert or bcl2fastq from Illumina.
  • Identify the appropriate Space Ranger pipeline based on sample type, species, and imaging modality. Pipeline constraints that are species-specific (humans indicated by # ) or sample type-specific (FFPE indicated by * ) are noted below.
  • Species: human#, mouse, others
  • Imaging type and automatic fiducial alignment
  • Compatible analysis pipelines
    • spaceranger count: Spatial GEX, Targeted GEX
    • spaceranger targeted-compare#: Targeted GEX
    • spaceranger targeted-depth#: Targeted GEX
    • spaceranger mkref: for custom references
  • Species: human, mouse
  • Imaging type and automatic fiducial alignment
  • Compatible analysis pipelines
    • spaceranger count: Spatial GEX
  • Species: human, mouse, others
  • Imaging type and automatic fiducial alignment
  • Compatible analysis pipelines
    • spaceranger count: Spatial GEX
    • spaceranger count: Spatial GEX for FFPE*
    • spaceranger aggr: samples processed using same protocol only
    • spaceranger mkref: for custom references

Fresh frozen (FF) and Fixed Frozen are probe-based whole transcriptome profiling assays.

  • Species: human, mouse
  • Imaging type and automatic fiducial alignment
    • CytAssist-captured brightfield image: supported
    • Microscope-captured fluorescence or brightfield image: supported (optionally, use manual image registration and/or manual fiducial alignment in Loupe Browser)
  • Compatible analysis pipelines
    • spaceranger count: CytAssist GEX