Purdue University

Commands

• ngsutils
• bamutils
• bedutils
• fastqutils
• gtfutils

Module

You can load the modules by:

module load biocontainers
module load ngsutils

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 Ngsutils on our clusters:

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

module --force purge
ml biocontainers ngsutils

bamutils filter \
    input.bam \
    MQ10filtered.bam  \
    -mapped \
    -noqcfail \
    -gte MAPQ 10

bamutils stats \
   -gtf genome.gtf MQ10filtered.bam \ 
   > MQ10filtered_bamstats