STAR RNA-seq Aligner Skill

SkillMonitoring & ops

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

Instructions available. Your AI can read the instructions. Execution depends on the setup they require.

Account requirements not reviewed. Check the skill instructions before use; ahel provides instructions and does not run this skill.

Add ahel to your AI once: Claude, ChatGPT, Cursor, Claude Code or Codex. Then ask it to use this.

Then ask your AI: use the STAR RNA-seq Aligner Skill skill

What this skill tells your AI

The instructions your AI receives, as published by a5c-ai/babysitter in library/specializations/domains/science/bioinformatics/skills/star-rnaseq-aligner/SKILL.md and read by ahel’s review.

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)

Signals

GitHub stars: 2k
Forks: 112
Last commit: Sep 2026

Advanced

Item type: skill
Key: star-rnaseq-aligner
Source: github.com/a5c-ai/babysitter

github.com/a5c-ai/babysitter