star-ssse3

name	star-ssse3
description	Use when aligning RNA-seq reads to a reference genome or generating splice-aware genome indices for transcript alignment.
disable-model-invocation	true
user-invocable	true

star-ssse3

Quick Start

• Command: STAR-ssse3
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/STAR-ssse3
• Full reference: See 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 STAR, BAM-input, or lift-over modes with the SSSE3-optimized STAR binary.
• Generate splice-junction-aware mappings for downstream counting, transcript assembly, or QC.

Common Patterns

# 1) Build a STAR genome index
STAR-ssse3 \
  --runMode genomeGenerate \
  --genomeDir star_index \
  --genomeFastaFiles genome.fa \
  --sjdbGTFfile genes.gtf \
  --runThreadN 16

# 2) Align paired-end gzipped RNA-seq reads
STAR-ssse3 \
  --genomeDir star_index \
  --readFilesIn sample_R1.fastq.gz sample_R2.fastq.gz \
  --readFilesCommand zcat \
  --runThreadN 16

# 3) Align and emit coordinate-sorted BAM
STAR-ssse3 \
  --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 using --runMode genomeGenerate with --genomeDir, --genomeFastaFiles, and optional --sjdbGTFfile
2. Align reads using --runMode alignReads with --genomeDir pointing to the index and --readFilesIn specifying input files
3. Set --runThreadN to match available CPU cores for parallel processing
4. Review alignment outputs (BAM) and splice junction files (SJ.out.tab) in the output directory

Guardrails

• Use genome indices generated with STAR version 2.7.4a or later; older indices are incompatible
• Provide uncompressed FASTA/FASTQ input files, or use --readFilesCommand (e.g., zcat) for compressed files
• Specify --genomeLoad NoSharedMemory unless you explicitly manage shared memory genome loading across runs