star-rna-seq-alignerlisted

# 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 - **Software**: STAR ≥ 2.7.0 (conda or compiled binary) - **Reference files**: genome FASTA + GTF annotation (same assembly) - **RAM**: 30–32 GB for human/mouse genome index; 8–16 GB for smaller genomes - **Disk**: ~25 GB for human genome index, ~5–10