Get Regional Methylation

The Get Regional Methylation task uses a region annotation (.bed) file to generate regions from CpG methylation count data. For each region specified in the annotation file, methylation counts of all CpG sites within the region are averaged to produce a count value in a regions-by-samples count matrix.

Using a built-in promoter regions file

A built-in annotation model based on human (hg38) promoter regions from ENSEMBL version 114 is provided. To invoke Get Regional Methylation task,

• Click on 5-base Methylation data node.

• Select Region analysis from context-sensitive menu, select Get Regional Methylation.

• Select an annotation model from Assembly and Annotation model drop-down, then click Finish.

Using a custom regions file

When you have a list of regions of interest, you may upload a custom region bed file for the Get Regional Methylation task. The custom regions file should:

• Consists of 3 columns: chromosome, start position, and stop position. The positions should be 0-based coordinates.

• No columns name.

• Tab-delimited.

• Saved as .bed file.

After the custom region file is prepared, following these steps to apply it on the Get Regional Methylation task:

• Click on 5-base Methylation data node.

• Select Region analysis from context-sensitive menu, select Get Regional Methylation.

• Select an Assembly, and select Add Annotation model from Annotation model drop-down.

• In Add annotation file dialog, select Add Annotation model from Annotation model drop-down, type in a name for the custom annatation, select Import annotation file, then click Create.

• At Select file page, select My Computer.

• Click + Choose button to choose a .bed file from your computer.

• The selected file name will be displayed, click Next.

• Select Other for Annotation type, click Next.

• Click Finish to run Get Regional Methylation based on the selected custom regions file.