STAR
Introduction
STAR
: ultrafast universal RNA-seq aligner.
Detailed usage can be found here: https://github.com/alexdobin/STAR
Versions
2.7.10a
2.7.10b
2.7.9a
Commands
STAR
STARlong
Module
You can load the modules by:
module load biocontainers
module load star/2.7.10a
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 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