starlong-plain

name	starlong-plain
description	Use when aligning long RNA-seq reads (PacBio, Nanopore) to a reference genome using splice-aware mapping with STARlong.
disable-model-invocation	true
user-invocable	true

starlong-plain

Quick Start

• Command: STARlong-plain --genomeDir /path/to/index --readFilesIn reads.fastq
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/STARlong-plain
• Full reference: See references/help.md for complete options and parameters

When To Use This Tool

• Align long RNA-seq reads from PacBio or Nanopore with STARlong.
• Build or reuse STAR-compatible genome indices for long-read splice-aware mapping.
• Map full-length transcript reads while keeping STAR-style splice-junction outputs.
• Run a long-read-focused STAR wrapper instead of the short-read defaults.

Common Patterns

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

# 2) Align long reads from FASTQ
STARlong-plain \
  --genomeDir starlong_index \
  --readFilesIn longreads.fastq \
  --runThreadN 16

# 3) Align gzipped long reads and emit sorted BAM
STARlong-plain \
  --genomeDir starlong_index \
  --readFilesIn longreads.fastq.gz \
  --readFilesCommand zcat \
  --outSAMtype BAM SortedByCoordinate \
  --runThreadN 16

Recommended Workflow

1. Prepare genome FASTA and optionally GTF annotation for splice junctions
2. Generate genome index: STARlong-plain --runMode genomeGenerate --genomeDir ./index --genomeFastaFiles genome.fa --sjdbGTFfile annotations.gtf
3. Align long reads: STARlong-plain --genomeDir ./index --readFilesIn reads.fastq
4. Collect output alignments (SAM/BAM) and splice junction files from the output directory

Guardrails

• Genome FASTA files must be plain text, not compressed
• --genomeSAindexNbases may need scaling for small genomes: min(14, log2(GenomeLength)/2 - 1)
• Specify shell explicitly with --sysShell /bin/bash if default shell fails
• Compressed read input still requires --readFilesCommand zcat or an equivalent decompressor