# Star Rnaseq Aligner

> Star Rnaseq Aligner is an Agent Skill for documents published in the a5c-ai/babysitter repository on GitHub: a SKILL.md instruction file an AI agent can load to do this task.

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

- Skill name: `star-rnaseq-aligner`
- Category: [Documents](https://www.openparable.com/skill/documents/1)
- Source: https://github.com/a5c-ai/babysitter/blob/HEAD/library/specializations/domains/science/bioinformatics/skills/star-rnaseq-aligner/SKILL.md
- Repository: a5c-ai/babysitter (1,548 GitHub stars when collected)

## SKILL.md

# 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)

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Source: https://www.openparable.com/skill/documents/star-rnaseq-aligner (OpenParable). Cite the canonical URL above.