SAW User Manual V8.0
  • Overview
  • Getting Started
    • Introduction
    • Glossary
  • Download Center
  • Analysis
    • Inputs
      • Chip mask
      • FASTQs
      • Images
    • Pipelines
      • SAW commands
      • count
        • Stereo-seq T FF
        • Stereo-seq N FFPE
    • Outputs
      • count outputs
      • realign outputs
      • HTML report
      • BAM
      • Matrices
      • Images
      • Analysis
  • Tutorials
    • Preparation of reference
    • Stereo-seq FF
    • Stereo-seq FFPE
    • With manually processed files
    • Secondary analysis
    • Format conversion
  • Algorithms
    • Read processing algorithms
    • Image processing algorithms
  • Advanced
    • Analysis with GPU
    • Expression matrix format
    • Image-related record format
  • Release Notes
  • SUPPORT PAGES
    • Datasets
    • Troubleshooting
    • Software and Kit Compatibility
    • Q & A
    • StereoMap
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  • New to SAW?
  • SAW workflow

Getting Started

Last updated 9 months ago

New to SAW?

What is SAW? Stereo-seq Analysis Workflow (SAW) software suite is a set of pipelines bundled to map sequenced reads to their spatial location on the tissue section, quantify spatial feature expression, and visually present spatial expression distribution.

For further details regarding STOmics and SAW, click the title.

SAW workflow

Set up

Download software >

Installation >

Input datasets

Input overview >

Learn about pipelines

SAW commands >

SAW count >

SAW realign >

Complementary ones >

Stereo-seq FF >

Stereo-seq FFPE >

Manual processing >

Output overview >

HTML report >

Glossary >

Algorithms >

File format >

With GPU >

Run analysis

Review outputs

Other information