metilene

metilene is a software tool to annotate differentally methylated regions (DMRs) and differentially methylated CpG sites (DMCs) from Methyl-seq data. metilene accounts for intra-group variances and offers different modes de-novo DMR detection, DMR detection within a known set of genomic features, and DMC detection. Various biological data can be used, metilene works with Whole-genome Bisulfite Sequencing (WGBS), Reduced representation bisulfite sequencing (RRBS), and any other input data, as long as absolute (methylation) levels and genomic coordinates are provided. metilene uses a circular binary segmentation and a 2D-KS test to call DMRs. Adjsuted p-values are calculated using the Bonferroni correction.

Availability and Restrictions

Versions

The following versions of bedtools are available on OSC clusters:

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

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

Access

metilene is available to all OSC users without restriction.

Publisher/Vendor/Repository and License Type

Frank Jühling, Helene Kretzmer, Stephan H. Bernhart, Christian Otto, Peter F. Stadler & Steve Hoffmann, GNU GPL v2.0 license

Usage

Usage on Owens

Set-up

To configure your environment for use of metilene, run the following command: module load metilene. The default version will be loaded. To select a particular metileneversion, use module load metilene/version. For example, use module load metilene/2.7 to load metilene 2.7.

Usage on Pitzer

Set-up

To configure your environment for use of metilene, run the following command: module load metilene. The default version will be loaded. To select a particular metileneversion, use module load metilene/version. For example, use module load metilene/2.7 to load metilene 2.7.

Further Reading

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