BISMARK

Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.

Bismark requires Bowtie or Bowtie2. For BAM output, SAMtools is required.

Documentation

Usage on Bridges-2

To see what versions of Bismark are available and if there is more than one, which is the default, along with some help, type

module spider bismark

To use Bismark, include a command like this in your batch script or interactive session to load the Bismark module: (note ‘module load’ is case-sensitive):

module load bismark

Usage on Bridges

To see what versions of Bismark are available type

module avail bismark

To see what other modules are needed, what commands are available and how to get additional help type

module help bismark

To use Bismark, include a command like this in your batch script or interactive session to load the Bismark module:

module load bismark

Be sure you also load any other modules needed, as listed by the module help bismark command.