Methyldackel

Introduction

MethylDackel (formerly named PileOMeth, which was a temporary name derived due to it using a PILEup to extract METHylation metrics) will process a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments and extract per-base methylation metrics from them. MethylDackel requires an indexed fasta file containing the reference genome as well.

For more information, please check:

Versions

  • 0.6.1

Commands

  • MethylDackel

Module

You can load the modules by:

module load biocontainers
module load methyldackel

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 methyldackel on our clusters:

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

module --force purge
ml biocontainers methyldackel

MethylDackel extract chgchh.fa chgchh_aln.bam