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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 latest 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 job

Serial Job

Here is an example job using 2 cores and 3G memory:

#!/bin/sh
#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_rt=1:0:0
#$ -l h_vmem=1.5G

module load bismark

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

References