Transrate

Introduction

Transrate is software for de-novo transcriptome assembly quality analysis.

For more information, please check:

Docker hub: https://hub.docker.com/r/arnaudmeng/transrate

Home page: http://hibberdlab.com/transrate/

Versions

• 1.0.3

Commands

• transrate

Module

You can load the modules by:

module load biocontainers
module load transrate

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 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