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 running on 1 core and 2GB of memory:
#!/bin/bash
#$ -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 running on 4 cores and 20GB of memory with optimal performance:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 4
#$ -l h_rt=240:0:0
#$ -l h_vmem=5G
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}