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name: cellranger-processor description: Cell Ranger skill for 10X Genomics single-cell data processing allowed-tools:

• Read
• Write
• Glob
• Grep
• Edit
• WebFetch
• WebSearch
• Bash metadata: version: "1.0" category: bioinformatics tags:
  • transcriptomics
  • single-cell
  • 10x-genomics
  • demultiplexing graph: domains: [domain:bioinformatics] specializations: [specialization:biomedical-informatics] skillAreas: [skill-area:python-data-pipelines, skill-area:data-analysis, skill-area:statistical-analysis] workflows: [workflow:experiment-design] roles: [role:research-engineer, role:biomedical-engineer]

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CellRanger Processor Skill

Purpose

Provide Cell Ranger capabilities for 10X Genomics single-cell data processing including demultiplexing and alignment.

Capabilities

• BCL to FASTQ conversion
• Cell barcode demultiplexing
• UMI counting
• Feature barcode processing
• Aggregate sample analysis
• Loupe Browser file generation

Usage Guidelines

• Configure sample sheets accurately
• Validate cell counts against expectations
• Review QC metrics from web summary
• Aggregate samples for combined analysis
• Generate Loupe files for visualization
• Document reference versions

Dependencies

• Cell Ranger
• STARsolo

Process Integration

• Single-Cell RNA-seq Analysis (scrnaseq-analysis)
• Spatial Transcriptomics Analysis (spatial-transcriptomics)