isoseq3
Link to section 'Introduction' of 'isoseq3' Introduction
Isoseq3 - Scalable De Novo Isoform Discovery.
For more information, please check its website: https://biocontainers.pro/tools/isoseq3 and its home page on Github.
Link to section 'Versions' of 'isoseq3' Versions
- 3.4.0
- 3.7.0
- 3.8.2
Link to section 'Commands' of 'isoseq3' Commands
- isoseq3
Link to section 'Module' of 'isoseq3' Module
You can load the modules by:
module load biocontainers
module load isoseq3
Link to section 'Example job' of '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