Purdue University

Commands

• STAR-Fusion

Module

You can load the modules by:

module load biocontainers
module load starfusion

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-Fusion on our clusters:

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

module --force purge
ml biocontainers starfusion

STAR-Fusion --CPU 24 --left_fq ../star/SRR12095148_1.fastq --right_fq  ../star/SRR12095148_2.fastq\
     --genome_lib_dir  GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir \
     --FusionInspector validate \
     --denovo_reconstruct \
     --examine_coding_effect \
     --output_dir STAR-Fusion-output