Finding differentially methylated regions

The Targeted Methyl application of the QIAseq Panel Analysis Assistant (see QIAseq Panel Analysis Assistant) offers a "Detect Differentially Methylated Regions" tool to be run after the Detect QIAseq Methylation workflow. The tool requires at least two case and two control samples.

Click Run to open the tool's wizard. In the first dialog, select the case read mappings, and click Next.

In the following dialog you can optionally choose to provide target regions. If these are supplied, then each target is separately tested for differential methylation. It makes sense to provide targets if they are the unit of biological interest, or if they are short enough that methylation patterns within a target are expected to be constant i.e. most Cs are hypomethylated/hypermethylated/unchanged when compared to a control sample. If no target regions are provided, the tool will search for differential methylation by dividing the genome into 1kb regions.

In the final dialog, select the control read mappings. The output of the tool is a track of differentially methylated regions for CpG sites.

The above-described tool works by calling the Call Methylation Levels tool (see with parameters optimized for QIAseq Targeted Methyl data. To run the Call Methylation Levels tool directly with these optimized parameters: