Purdue University

Commands

• STAR
• STARlong

Module

You can load the modules by:

module load biocontainers
module load star/2.7.10a 

Example job

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 our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=star
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers star/2.7.10a


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