star-rnaseq-aligner

# 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)