Metilene

Description

metilene website

metilene is a software tool to annotate differentally methylated regions (DMRs) and differentially methylatedcytosine sites (DMCs) from Methyl-Seq data. metilene accounts for intra-group variances and offers differentmodes de-novo DMR detection, DMR detection within a known set of genomic features, and DMC detection.Various biological data can be used, metilene works for Whole-Genome Bisulfite Sequencing (WGBS), Re-duced Representation Bisulfite Sequencing (RRBS), and any other input data, as long as absolute (methyla-tion) levels and genomic coordinates are provided. metilene uses a circular binary segmentation and a 2D-KStest to call DMRs. Adjusted p-values are calculated using the Bonferroni or Benjamini-Hochberg correction(see option-c,--mtc).

Environment Modules

Run module spider metilene to find out what environment modules are available for this application.

Environment Variables

• HPC_METILENE_DIR - installation directory

Citation

If you publish research that uses metilene you have to cite it as follows:

Jühling, F., Kretzmer, H., Bernhart, S. H., Otto, C., Stadler, P. F., & Hoffmann, S. (2016). metilene: Fast and sensitive calling of differentially methylated regions from bisulfite sequencing data. Genome Research, 26(2), 256–262. https://doi.org/10.1101/gr.196394.115

Categories

biology, genomics, methylation