star-plain

name	star-plain
description	Use when aligning RNA-seq reads to a reference genome with splice-aware mapping, generating genome indices, or performing related operations like lift-over and BAM input processing.
disable-model-invocation	true
user-invocable	true

star-plain

Quick Start

• Command: STAR-plain
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/STAR-plain
• 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.
• Lift over annotations between assemblies or process BAM input with STAR run modes.
• Generate splice-junction-aware mappings for downstream counting, transcript assembly, or QC.

Common Patterns

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

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

# 3) Align and emit coordinate-sorted BAM
STAR-plain \
  --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-plain --runMode genomeGenerate --genomeDir /path/to/index --genomeFastaFiles genome.fa --sjdbGTFfile annotations.gtf --runThreadN N
2. Align reads: STAR-plain --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. Review output: check alignment results and splice junction file SJ.out.tab

Guardrails

• Genome FASTA files must be plain text and cannot be zipped
• Scale --genomeSAindexNbases down for small genomes: use min(14, log2(GenomeLength)/2 - 1)
• Use --genomeLoad NoSharedMemory for isolated runs to avoid shared memory issues on some systems
• Compressed read files need an explicit decompression command such as --readFilesCommand zcat