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Cell Ranger

Supported Tool

Summarise quality metrics from Cell Ranger count and vdj.


The Cell Ranger module parses the quality reports generated by Cell Ranger (tested on Cell Ranger 6) and summarise the main information useful for QC, including:

  • sequencing metrics
  • mapping metrics
  • estimated number of cells and reads / cell
  • UMI counts
  • mean detect genes per cell
  • antibody cell counts and distribution

Note that information such as clustering and differential expression are not reported.

The input files are web summaries generated by Cell Ranger. Expected file names are *web_summary.html. Sample IDs are parsed directly from the reports and the module will automatically recognize if they are generated from VDJ or count analysis.

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

File search patterns

  - fn: "*.html"
    contents: '"command":"Cell Ranger","subcommand":"count"'
    num_lines: 13
  - fn: "*.html"
    contents: '"command": "Cell Ranger", "subcommand": "count"'
    num_lines: 13
  - fn: "*.html"
    contents: '"command":"Cell Ranger","subcommand":"vdj"'
    num_lines: 13
  - fn: "*.html"
    contents: '"command": "Cell Ranger", "subcommand": "vdj"'
    num_lines: 13