Software: MethylDackel
Description
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.
Available Versions
| Unspecified: | 0.6.1 |
|---|
BioContainers: https://biocontainers.pro/tools/methyldackel
Home page: https://github.com/dpryan79/MethylDackel
Commands
- MethylDackel
Module
You can load the modules by:
module load biocontainers
module load methyldackel
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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