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Cell Ranger ARC

note

Analyzes Single Cell Multiome ATAC + Gene Expression data produced by 10X Genomics

https://www.10xgenomics.com/support/software/cell-ranger-arc/latest

The module summarizes the main information from Cell Ranger ARC which is useful for QC:

  • sequencing metrics
  • cell metrics
  • targeting metrics
  • mapping metrics
  • atac TSS plots
  • atac insert size distribution plots
  • gex saturaiton plots
  • gex genes per cell plots

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

The input files are web summaries generated by Cell Ranger ARC. 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​

cellranger_arc:
  - contents: Cell Ranger ARC
    fn: "*.html"
    num_lines: 250