star-rnaseq-aligner
STAR alignment skill for splice-aware RNA-seq read mapping with comprehensive QC metrics
Best use case
star-rnaseq-aligner is best used when you need a repeatable AI agent workflow instead of a one-off prompt.
STAR alignment skill for splice-aware RNA-seq read mapping with comprehensive QC metrics
Teams using star-rnaseq-aligner should expect a more consistent output, faster repeated execution, less prompt rewriting.
When to use this skill
- You want a reusable workflow that can be run more than once with consistent structure.
When not to use this skill
- You only need a quick one-off answer and do not need a reusable workflow.
- You cannot install or maintain the underlying files, dependencies, or repository context.
Installation
Claude Code / Cursor / Codex
Manual Installation
- Download SKILL.md from GitHub
- Place it in
.claude/skills/star-rnaseq-aligner/SKILL.mdinside your project - Restart your AI agent — it will auto-discover the skill
How star-rnaseq-aligner Compares
| Feature / Agent | star-rnaseq-aligner | Standard Approach |
|---|---|---|
| Platform Support | Not specified | Limited / Varies |
| Context Awareness | High | Baseline |
| Installation Complexity | Unknown | N/A |
Frequently Asked Questions
What does this skill do?
STAR alignment skill for splice-aware RNA-seq read mapping with comprehensive QC metrics
Where can I find the source code?
You can find the source code on GitHub using the link provided at the top of the page.
SKILL.md Source
# 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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