Bismark

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

Availability and Restrictions

Versions

The following versions of bedtools are available on OSC clusters:

Version Owens Pitzer
0.22.1 X* X*
* Current default version

You can use module spider bismark to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

Bismark is available to all OSC users without restriction.

Publisher/Vendor/Repository and License Type

Babraham Bioinformatics, GNU GPL v3

Usage

Usage on Owens

Set-up

To configure your environment for use of metilene, run the following command: module load bismark. The default version will be loaded. To select a particular Bismark version, use module load bismark/version. For example, use module load bismark/0.22.1 to load Bismark 0.22.1.

Usage on Pitzer

Set-up

To configure your environment for use of metilene, run the following command: module load bismark. The default version will be loaded. To select a particular Bismark version, use module load bismark/version. For example, use module load bismark/0.22.1 to load Bismark 0.22.1.

Further Reading

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