bismark
Link to section 'Description' of 'bismark' Description
A tool to map bisulfite converted sequence reads and determine cytosine methylation states
Link to section 'Versions' of 'bismark' Versions
- Anvil: 0.23.0
Link to section 'Commands' of 'bismark' Commands
- bam2nuc
- bismark
- bismark2bedGraph
- bismark2report
- bismark2summary
- bismark_genome_preparation
- bismark_methylation_extractor
- coverage2cytosine
- deduplicate_bismark
- filter_non_conversion
- NOMe_filtering
Link to section 'Module' of 'bismark' Module
You can load the modules by:
module load bismark
Link to section 'Example job' of 'bismark' Example job
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 load bismark
bismark_genome_preparation --bowtie2 data/ref_genome
bismark --multicore 12 --genome data/ref_genome seq.fastq