star-alignment

What problem does it solve?

This Skill aligns RNA-seq reads with STAR, a powerful aligner for novel junction discovery, providing 2-pass mapping and genome-generation strategies.

Core Features & Use Cases

• Splice-aware Alignment: Aligns RNA-seq reads with high sensitivity to novel junctions.
• 2-pass Mapping: Offers 2-pass mapping for sensitive novel junction discovery.
• Genome Generation: Generates genome index for alignment.
• Use Case: Ideal for bulk RNA-seq with novel junction discovery, single-cell RNA-seq, chimeric/fusion detection, and long-read cDNA/ONT direct RNA.

Quick Start

Generate the genome index with 'STAR --runMode genomeGenerate' and align reads with 'STAR --runMode alignReads'.