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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

Performance issues when using the Bowtie2 aligner

To avoid poor performance and threading issues when running Bismark with the Bowtie2 aligner, please use the -p option with a value of half the number of cores requested and do not use the --multicore option.

See the example jobs below for more information.

Request an even number of cores when using the Bowtie2 aligner

To ensure Bismark runs with optimal performance, always request an even number of cores when running Bismark with the Bowtie2 aligner, to ensure the -p option is populated correctly.

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 optimal performance:

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

module load bismark

# Fork the Bowtie2 aligner by half the number of cores requested
# to avoid poor performance and threading issues
REPCORES=$((NSLOTS / 2))

bismark \
    --genome_folder <genome_folder> \
    -1 fasta1.fq.gz \
    -2 fasta2.fq.gz \
    -p $REPCORES

References