name: star-rnaseq-aligner description: STAR alignment skill for splice-aware RNA-seq read mapping with comprehensive QC metrics allowed-tools:

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• Bash metadata: version: "1.0" category: bioinformatics tags:
  • transcriptomics
  • alignment
  • rna-seq
  • splice-aware

STAR RNA-seq Aligner Skill

Purpose

Provide STAR alignment for splice-aware RNA-seq read mapping with comprehensive QC metrics.

Capabilities

• Splice junction detection
• Two-pass alignment mode
• Chimeric read detection (fusions)
• Gene quantification (--quantMode)
• Custom genome index generation
• Output in multiple formats

Usage Guidelines

• Generate genome indices with annotation
• Use two-pass mode for novel junction discovery
• Enable chimeric read detection for fusion analysis
• Generate quantification in addition to alignments
• Optimize parameters for read length
• Document STAR version and parameters

Dependencies

• STAR
• HISAT2
• kallisto

Process Integration

• RNA-seq Differential Expression Analysis (rnaseq-differential-expression)
• Single-Cell RNA-seq Analysis (scrnaseq-analysis)
• Spatial Transcriptomics Analysis (spatial-transcriptomics)