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. If you have any questions, please contact OSC Help.

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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