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Bismark

Bismark is a tool for mapping bisulfite converted sequence reads and determining cytosine methylation states

Bismark is available as a module on Apocrita.

Usage

To run the default installed version of Bismark, simply load the bismark module:

$ module load bismark
$ bismark -h

Usage:   bismark [options] \
                 --genome <genome_folder> \
                 {-1 <mates1> -2 <mates2> | <singles>}

For full usage documentation, run bismark -h.

Example jobs

Running with multiple cores

Please be aware that running Bismark with multiple cores can cause threading issues when used with the -p option. To avoid this please ensure you use the --multicore ${NSLOTS} option instead.

Serial jobs

Here is an example job using 1 core and 2G memory:

#!/bin/sh
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G

module load bismark

# Prepare FASTA genomes stored in <dir>
# Output is stored in <dir>
bismark_genome_preparation <dir>

Here is an example job using 4 cores and 20G memory with the multicore option:

#!/bin/bash
#$ -pe smp 4
#$ -l h_vmem=5G
#$ -l h_rt=24:0:0
#$ -cwd
#$ -j y

module load bismark

bismark --multicore ${NSLOTS} \
        --genome_folder <genome_folder> \
        -1 <mates1> -2 <mates2>

References