star-sse3

name	star-sse3
description	Use when aligning RNA-seq reads to a reference genome with splice-aware mapping, generating genome indexes, or performing splice junction detection.
disable-model-invocation	true
user-invocable	true

star-sse3

Quick Start

• Command: STAR-sse3 --genomeDir /path/to/index --readFilesIn reads.fq
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/STAR-sse3
• Full reference: See references/help.md for complete options and parameter details

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 SSE3-optimized STAR binary.
• Generate splice-junction-aware mappings for downstream counting, transcript assembly, or QC.

Common Patterns

# 1) Build a STAR genome index
STAR-sse3 \
  --runMode genomeGenerate \
  --genomeDir star_index \
  --genomeFastaFiles genome.fa \
  --sjdbGTFfile genes.gtf \
  --runThreadN 16

# 2) Align paired-end gzipped RNA-seq reads
STAR-sse3 \
  --genomeDir star_index \
  --readFilesIn sample_R1.fastq.gz sample_R2.fastq.gz \
  --readFilesCommand zcat \
  --runThreadN 16

# 3) Align and emit coordinate-sorted BAM
STAR-sse3 \
  --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 using FASTA files and optional GTF annotations
2. Align reads with --runMode alignReads specifying --genomeDir and --readFilesIn
3. Set --runThreadN to match available CPU cores for parallel processing
4. Collect aligned BAM output and splice junction files from the output directory

Guardrails

• Genome index must exist before alignment; generate it first with --runMode genomeGenerate
• Compressed input files require --readFilesCommand (e.g., zcat for .gz files)
• Ensure --genomeSAindexNbases is scaled appropriately for small genomes