transrate
Link to section 'Introduction' of 'transrate' Introduction
Transrate is software for de-novo transcriptome assembly quality analysis.
Docker hub: https://hub.docker.com/r/arnaudmeng/transrate
Home page: http://hibberdlab.com/transrate/
Link to section 'Versions' of 'transrate' Versions
- 1.0.3
Link to section 'Commands' of 'transrate' Commands
- transrate
Link to section 'Module' of 'transrate' Module
You can load the modules by:
module load biocontainers
module load transrate
Link to section 'Example job' of 'transrate' 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 transrate on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=transrate
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers transrate
transrate --assembly mm10/Mus_musculus.GRCm38.cds.all.fa \
--left seq_1.fq.gz \
--right seq_2.fq.gz \
--threads 12