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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  • SAW count
  • Stereo-seq T FF
  • Stereo-seq N FFPE
  1. Analysis
  2. Pipelines

count

SAW count

SAW count is the central component of the software suite, compatible with most Stereo-seq FF and Stereo-seq FFPE datasets. The inputs consist of a chip mask, FASTQ files, a reference and a microscope image. So that the pipeline counts gene expression reads to generate expression matrices and analysis results from the Stereo-seq chip.

According to the STOmics product lines, parameter usage varies lightly. Before performing an analysis on SAW count, pay attention to the information regarding your assay kit version. Choose the appropriate one.

Stereo-seq T FF

*T stands for Chip T

Count for Stereo-seq T FF V1.2 Spatial Gene Expression

Coming soon...

Stereo-seq N FFPE

*N stands for Chip N

Count for Stereo-seq N FFPE V1.0 Spatial Gene Expression

Last updated 9 months ago