methyldackel
Link to section 'Introduction' of '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.
BioContainers: https://biocontainers.pro/tools/methyldackel
Home page: https://github.com/dpryan79/MethylDackel
Link to section 'Versions' of 'methyldackel' Versions
- 0.6.1
Link to section 'Commands' of 'methyldackel' Commands
- MethylDackel
Link to section 'Module' of 'methyldackel' Module
You can load the modules by:
module load biocontainers
module load methyldackel
Link to section 'Example job' of 'methyldackel' 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 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