star-rnaseq-aligner

name	star-rnaseq-aligner
description	STAR alignment skill for splice-aware RNA-seq read mapping with comprehensive QC metrics
allowed-tools	["Read","Write","Glob","Grep","Edit","WebFetch","WebSearch","Bash"]
metadata	{"version":"1.0","category":"bioinformatics","tags":["transcriptomics","alignment","rna-seq","splice-aware"]}

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)