star-avx

name	star-avx
description	Use when aligning RNA-seq reads to a reference genome with splice-aware mapping, generating genome indices, or processing single-cell RNA-seq data with STARsolo.
disable-model-invocation	true
user-invocable	true

star-avx

Quick Start

• Command: STAR-avx [options] --genomeDir /path/to/genome/index/ --readFilesIn R1.fq R2.fq
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/STAR-avx
• Full reference: references/help.md

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 STARsolo, BAM-input, or lift-over modes with the AVX-optimized STAR binary.
• Generate splice-junction-aware mappings for downstream counting, transcript assembly, or QC.

Common Patterns

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

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

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

Recommended Workflow

1. Generate a genome index using --runMode genomeGenerate with --genomeFastaFiles and --sjdbGTFfile
2. Align reads with --runMode alignReads specifying --genomeDir and --readFilesIn
3. Set appropriate thread count with --runThreadN based on available cores
4. Review output alignments (SAM/BAM) and splice junction files (SJ.out.tab)

Guardrails

• Genome index must be compatible with STAR version 2.7.4a or later (versionGenome parameter)
• Ensure --genomeSAindexNbases is scaled appropriately for small genomes: min(14, log2(GenomeLength)/2 - 1)
• Use --readFilesCommand zcat for compressed .gz input files; FASTA/FASTQ inputs cannot be zipped directly