Purdue University

Commands

• TEtranscripts
• TEcount

Module

You can load the modules by:

module load biocontainers
module load tetranscripts

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 Tetranscripts on our clusters:

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

module --force purge
ml biocontainers tetranscripts

TEtranscripts --format BAM --mode multi \
    -t treatment_sample1.bam treatment_sample2.bam treatment_sample3.bam \
    -c control_sample1.bam control_sample2.bam control_sample3.bam \
    --GTF genic-GTF-file \
    --GTF genic-GTF-file \  
    --project sample_nosort_test