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star-rnaseq-aligner

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

QUICK START

How to use this skill

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Source SKILL.md: https://github.com/a5c-ai/babysitter/blob/HEAD/library/specializations/domains/science/bioinformatics/skills/star-rnaseq-aligner/SKILL.md

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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)