STAR-Fusion¶
Introduction¶
STAR-Fusion
is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT).
For more information, please check its | Docker hub: https://hub.docker.com/r/trinityctat/starfusion and its home page on Github.
Versions¶
1.11b
Commands¶
STAR-Fusion
Module¶
You can load the modules by:
module load biocontainers
module load starfusion
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-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