Modbam2bed

Introduction

Modbam2bed is a program to aggregate modified base counts stored in a modified-base BAM file to a bedMethyl file.

For more information, please check:

Docker hub: https://hub.docker.com/r/zeunas/modbam2bed

Home page: https://github.com/epi2me-labs/modbam2bed

Versions

• 0.9.1

Commands

• modbam2bed

Module

You can load the modules by:

module load biocontainers
module load modbam2bed

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 modbam2bed on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=modbam2bed
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers modbam2bed