Star

Introduction

STAR (Spliced Transcripts Alignment to a Reference) is an ultrafast universal RNA-seq aligner.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/star
Home page: https://github.com/alexdobin/STAR

Versions

  • 2.7.10a

  • 2.7.10b

  • 2.7.9a

Commands

  • STAR

  • STARlong

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run star on our clusters:

#!/bin/bash
#SBATCH -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 24
#SBATCH --job-name=star
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load star/XXXX ### you can run *module avail star* to check all available versions

STAR  --runThreadN 24  --runMode genomeGenerate  --genomeDir ref_genome  --genomeFastaFiles ref_genome.fasta

STAR --runThreadN 24 --genomeDir ref_genome --readFilesIn seq_1.fastq seq_2.fastq  --outSAMtype BAM SortedByCoordinate --outWigType wiggle read2