Bismark

Introduction

Bismark is a tool to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.

For more information, please check its website: https://biocontainers.pro/tools/bismark and its home page on Github.

Versions

  • 0.23.0

  • 0.24.0

Commands

  • bismark

  • bam2nuc

  • bismark2bedGraph

  • bismark2report

  • bismark2summary

  • bismark_genome_preparation

  • bismark_methylation_extractor

  • copy_bismark_files_for_release.pl

  • coverage2cytosine

  • deduplicate_bismark

  • filter_non_conversion

  • methylation_consistency

Dependencies

Bowtie v2.4.2, Samtools v1.12, HISAT2 v2.2.1 were included in the container image. So users do not need to provide the dependency path in the bismark parameter.

Module

You can load the modules by:

module load biocontainers
module load bismark

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 Bismark on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=bismark
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers bismark

bismark_genome_preparation --bowtie2 data/ref_genome

bismark --multicore 12 --genome data/ref_genome seq.fastq