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Space Ranger

Tool to analyze 10x Genomics spatial transcriptomics data

https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger

The module parses the quality reports generated by 10x Genomics Space Ranger (tested on Cell Ranger 2.1). Space Ranger has 2 main modules: count and vdj. The module summarises the main information useful for QC, including:

  • sequencing metrics
  • mapping metrics
  • estimated number of spots, and reads per spot.
  • detected genes per spot

Note that clustering results, differentially expressed genes and the images themselves are not reported.

The input files are web summaries generated by Space Ranger. Expected file names are *web_summary.html. Sample IDs are parsed directly from the reports.

If present in the original report, any warning is reported as well.

File search patterns​

spaceranger/count_html:
  - contents: '"command":"Space Ranger","subcommand":"count"'
    fn: "*.html"
    num_lines: 20
  - contents: '"command": "Space Ranger", "subcommand": "count"'
    fn: "*.html"
    num_lines: 20