This tool performs methylation analysis of sequencing data by comparing two conditions, e.g., control and treatment. One MEDIPS input file is needed for each condition. Currently, the tool works only with human data.
Based on the input data, a genome-wide coverage is calculated. The resolution for the coverage calculation can be set, and it is by default 50 bps. Smoothing of the resolution is recommended, and can be set separately from the coverage resolution. The default length for smoothing is 400 bp. Normalization is controlled using the setting for fragment length. Users can choose to calculate the enrichment of methylated CpG islands for promoter regions only, and select the length of the promoter region used. The default is 1000 bps upstream and 500 bps downstream from the transcription start site.
During the analysis, the whole genome or just the promoter regions are split into bins of coverage resolution (by default 50 bps). The short read coverage is calculated using this resolution. Since the short reads are not the whole length sonicated DNA fragments, smoothing of the results is usually performed by extending the reads. During the extension, each read is extended to both telomeric and sentromeric directions by the amount set in the smoothing extension parameter. For normalization the local CpG density needs to be estimated. The setting for fragment length specifies the area around each genomic bin that is used for calculating the local CpG density. The fragment length should be set close to the estimated size of the sonicated DNA fragments generated after the amplification.
If quality control plots are needed, the MEDIPS tool for one sample should be run separately for both conditions.
Results of the comparative methylation analysis are reported in the file methylation-comparison.tsv.
For more information about the functionality of the MEDIPS tool(s), see the manual on Bioconductor site at http://www.bioconductor.org/packages/2.7/bioc/html/MEDIPS.html.
If you publish results acquired using this tool, please site also Chavez et al., Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage, Genome Res. 2010 Oct;20(10):1441-50.