# Star Rnaseq Aligner

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

- Skill: `a5c-ai/star-rnaseq-aligner` (Agent Skill)
- Install (CLI): `npx skillmds@latest add a5c-ai/star-rnaseq-aligner`
- Raw SKILL.md: https://api.skillmd.com/api/skills/a5c-ai/star-rnaseq-aligner/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: a5c-ai (https://skillmd.com/u/a5c-ai)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/a5c-ai/star-rnaseq-aligner

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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)