star-avx2

name	star-avx2
description	Use when aligning RNA-seq reads to a reference genome or generating genome indices for spliced transcript alignment
disable-model-invocation	true
user-invocable	true

star-avx2

Quick Start

• Command: STAR-avx2
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/STAR-avx2
• Reference: See references/help.md for full options and parameters

When To Use This Tool

• Build STAR genome indices for RNA-seq alignment.
• Perform splice-aware alignment of short RNA-seq reads against a genome.
• Run STAR modes with the AVX2-optimized STAR binary.
• Generate splice-junction-aware mappings for downstream counting, transcript assembly, or QC.

Common Patterns

# 1) Build a STAR genome index
STAR-avx2 \
  --runMode genomeGenerate \
  --genomeDir star_index \
  --genomeFastaFiles genome.fa \
  --sjdbGTFfile genes.gtf \
  --runThreadN 16

# 2) Align paired-end gzipped RNA-seq reads
STAR-avx2 \
  --genomeDir star_index \
  --readFilesIn sample_R1.fastq.gz sample_R2.fastq.gz \
  --readFilesCommand zcat \
  --runThreadN 16

# 3) Align and emit coordinate-sorted BAM
STAR-avx2 \
  --genomeDir star_index \
  --readFilesIn sample_R1.fastq.gz sample_R2.fastq.gz \
  --readFilesCommand zcat \
  --outSAMtype BAM SortedByCoordinate \
  --runThreadN 16

Recommended Workflow

1. Generate genome index: STAR-avx2 --runMode genomeGenerate --genomeDir /path/to/index --genomeFastaFiles genome.fa --sjdbGTFfile annotations.gtf
2. Align reads: STAR-avx2 --genomeDir /path/to/index --readFilesIn R1.fq R2.fq --runThreadN N
3. Handle compressed input: Add --readFilesCommand zcat for .gz files or bzcat for .bz2 files
4. Check outputs: Review Aligned.out.sam for alignments and SJ.out.tab for splice junctions

Guardrails

• Set --runThreadN to match available CPU cores; default is 1 thread
• Ensure --sjdbOverhang equals read length minus 1 for optimal junction detection
• Use --genomeLoad NoSharedMemory on shared systems to avoid memory conflicts