star-sse4-1

name	star-sse4-1
description	Use when aligning RNA-seq reads to a reference genome, generating STAR genome indices, or performing splice-aware transcript alignment.
disable-model-invocation	true
user-invocable	true

star-sse4-1

Quick Start

• Command: STAR-sse4.1
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/STAR-sse4.1
• Full reference: See references/help.md for complete 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, lift-over, or BAM-input modes with the SSE4.1-optimized STAR binary.
• Generate splice-junction-aware mappings for downstream counting, transcript assembly, or QC.

Common Patterns

# 1) Build a STAR genome index
STAR-sse4.1 \
  --runMode genomeGenerate \
  --genomeDir star_index \
  --genomeFastaFiles genome.fa \
  --sjdbGTFfile genes.gtf \
  --runThreadN 16

# 2) Align paired-end gzipped RNA-seq reads
STAR-sse4.1 \
  --genomeDir star_index \
  --readFilesIn sample_R1.fastq.gz sample_R2.fastq.gz \
  --readFilesCommand zcat \
  --runThreadN 16

# 3) Align and emit coordinate-sorted BAM
STAR-sse4.1 \
  --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 with --runMode genomeGenerate, providing FASTA via --genomeFastaFiles and optional GTF via --sjdbGTFfile
2. Set --genomeDir to the index directory and configure threads with --runThreadN
3. Align reads using --runMode alignReads with input files specified via --readFilesIn
4. Collect output alignments (SAM/BAM) and splice junction files from the output directory

Guardrails

• Always provide --genomeDir pointing to a valid genome index before running alignment
• Set --runThreadN appropriately for available CPU cores to avoid resource contention
• Use --sjdbOverhang set to read length minus 1 for optimal splice junction detection