ReddRadar
Agent skill
star-rnaseq-aligner
STAR alignment skill for splice-aware RNA-seq read mapping with comprehensive QC metrics
Install this agent skill to your Project
npx add-skill https://github.com/a5c-ai/babysitter/tree/main/library/specializations/domains/science/bioinformatics/skills/star-rnaseq-aligner
Metadata
Additional technical details for this skill
- tags
-
transcriptomics alignment rna-seq splice-aware
- version
- 1.0
- category
- bioinformatics
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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