star

Quick Start

• Command: STAR
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/STAR
• Version: 2.7.11b
• Full reference: See references/help.md

When To Use This Tool

• Bulk RNA-seq or other splice-aware alignment against a genome index.
• One-time genome index generation before repeated RNA-seq alignments.
• Recovering splice junction evidence from SJ.out.tab and alignment QC from Log.final.out.
• Prefer STAR over subread-align when intron-spanning alignment is the main job.

Common Patterns

# 1) Build a STAR genome index once per reference/annotation pair
STAR \
  --runMode genomeGenerate \
  --runThreadN 16 \
  --genomeDir star_index \
  --genomeFastaFiles genome.fa \
  --sjdbGTFfile genes.gtf \
  --sjdbOverhang 149

# 2) Align paired-end gzipped RNA-seq reads and emit sorted BAM
STAR \
  --runThreadN 16 \
  --genomeDir star_index \
  --readFilesIn sample_R1.fastq.gz sample_R2.fastq.gz \
  --readFilesCommand zcat \
  --outSAMtype BAM SortedByCoordinate \
  --outFileNamePrefix sample.

# 3) Add simple gene-level quantification during alignment
STAR \
  --runThreadN 16 \
  --genomeDir star_index \
  --readFilesIn sample_R1.fastq.gz sample_R2.fastq.gz \
  --readFilesCommand zcat \
  --outSAMtype BAM SortedByCoordinate \
  --quantMode GeneCounts \
  --outFileNamePrefix sample.

Recommended Workflow

1. Build the index once with the exact genome FASTA and annotation you plan to quantify against.
2. Align reads with --genomeDir, --readFilesIn, and --readFilesCommand zcat for gzipped FASTQ.
3. Inspect Log.final.out, SJ.out.tab, and BAM size before moving into counting.
4. Count with featureCounts or another quantifier using the same annotation build.

Guardrails

• --genomeFastaFiles for genome generation must be plain-text FASTA, not gzipped FASTA.
• Set --sjdbOverhang to read length minus 1 for the library you are aligning.
• For small genomes, scale down --genomeSAindexNbases as documented in references/help.md.
• Keep chromosome naming consistent across FASTA, GTF, and downstream BAM-aware tools.