bismark
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'bismark' Versions
- 0.23.0
Link to section 'Commands' of 'bismark' 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
Link to section 'Dependencies' of 'bismark' 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.
Link to section 'Module' of 'bismark' Module
You can load the modules by:
module load biocontainers
module load bismark
Link to section 'Example job' of 'bismark' 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 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