Purdue University

Commands

• isoseq3

Module

You can load the modules by:

module load biocontainers
module load isoseq3

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 Isoseq3 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=isoseq3
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers isoseq3

isoseq3 --version

isoseq3 refine --require-polya \
    alz.demult.5p--3p.bam \
    primers.fasta alz.flnc.bam

isoseq3 cluster alz.flnc.bam \
    alz.polished.bam --verbose --use-qvs