Star Rnaseq Aligner
Documentsstar-rnaseq-alignerStar 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
QUICK START
How to use this skill
Bring this guide into your coding agent with a prompt tailored to the tool you use.
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Prompt to paste
Inspect the Agent Skill at https://github.com/a5c-ai/babysitter/blob/HEAD/library/specializations/domains/science/bioinformatics/skills/star-rnaseq-aligner/SKILL.md and all supporting files. Report provenance, permissions, scripts, dependencies, and security risks. Propose an exact installation into .agents/skills/star-rnaseq-aligner, but wait for my approval before writing files or running scripts.
Copying this prompt does not install or run the skill. Review third-party files before use.
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)