starfusion
Link to section 'Introduction' of 'starfusion' Introduction
STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT).
Docker hub: https://hub.docker.com/r/trinityctat/starfusion and its home page on Github.
Link to section 'Versions' of 'starfusion' Versions
- 1.11b
Link to section 'Commands' of 'starfusion' Commands
- STAR-Fusion
Link to section 'Module' of 'starfusion' Module
You can load the modules by:
module load biocontainers
module load starfusion
Link to section 'Example job' of '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