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