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