It is my first time analyzing a methylation dataset (sequenced with EM-seq). A collaborator suggested a method, but in previous studies the laboratory (previous researchers) used a different method.

The method uses the beta values and then follows a standard limma-voom pipeline.
When I process this data I arrive to a volcano plot that doesn't look well to me:

The "columns" on these p-values are weird, and do not seem related to any particular biology (gene, promoter, or region).

I saw that in a tutorial from here the m-values are used instead of beta, but they use also a chip-based assay instead of sequencing. I couldn't find any standard approach like the workflows for RNA-seq in methylation. Is there any bulk methylation sequencing but not array based tutorial?