cellranger-processor

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"]}

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)