STAR — Spliced RNA-seq Aligner

Overview

STAR (Spliced Transcripts Alignment to a Reference) aligns RNA-seq reads to a genome in a splice-aware manner, identifying novel and annotated splice junctions in a single pass. It generates coordinate-sorted BAM files compatible with samtools, IGV, deeptools, and GATK. STAR's 2-pass mode re-aligns reads using junctions discovered in the first pass, improving sensitivity for novel splice sites. With --quantMode GeneCounts, STAR simultaneously produces gene-level read count tables without requiring a separate featureCounts or HTSeq step.

When to Use

• Aligning bulk RNA-seq reads to a reference genome when downstream tools require a BAM file (variant calling, visualization, deeptools)
• Running ENCODE-compliant RNA-seq pipelines that mandate genome alignment
• Discovering novel splice junctions and alternative splicing events in the dataset
• Generating gene count tables alongside BAM alignment in a single step with --quantMode GeneCounts
• Processing long reads or reads with high mismatch rates by tuning --outFilterMismatchNmax
• Use Salmon instead when you only need transcript/gene quantification and do not need a BAM file — Salmon is 20-50× faster

Prerequisites