star-rna-seq-aligner

What problem does it solve?

This Skill automates the process of aligning RNA sequencing reads to a reference genome, a crucial step for analyzing gene expression and discovering novel transcripts.

Core Features & Use Cases

• Splice-aware Alignment: Accurately maps RNA reads, identifying both known and novel splice junctions.
• Genome Indexing: Generates necessary index files for efficient alignment.
• Output Generation: Produces coordinate-sorted BAM files, splice junction tables, and alignment statistics. Optionally generates gene count tables.
• Use Case: Analyze bulk RNA-seq data to identify differentially expressed genes by aligning raw reads to a reference genome and generating gene count matrices.

Quick Start

Align paired-end RNA-seq reads using the STAR aligner with a pre-generated genome index.