We use data from whole genome or reduced representation bisulfite sequencing to test for differential methylation between experimental groups. Our workflow relies on the nf-core methylseq pipeline to perform the alignment and methylation calling. This is followed by an in-house pipeline which tests for differential methylation at the level of individual CpGs and larger genomic regions.
A zip archive containing the results from an example analysis can be downloaded below. Please refer to the included README and the documentation for more details.