lmulroney
commented
3 months ago Hi @keenhl,
That will largely depend on the experimental set up and which two samples your are comparing.
In the case of a WT and a writer enzyme KO/KD, or an eraser over expression, the modification will likely be detected because a decrease in the manipulated sample.
In the case of a writer enzyme over expression or an eraser KD/KO, the modification will likely be detected due to an over abundance in the manipulated sample.
If you're comparing two different biological samples under different stress conditions, you need to know something about the modification mechanism in response to the stress a priori.
You can use the cluster counts to look at how the different samples were assigned to each cluster get a sense of which cluster was the modified cluster and which is the unmodified cluster depending on how the sample labels are distributed between the two clusters.
Sorry I couldn't be more direct, but it is hard to give precise advice without any details on your experimental design.
If a significant change in methylation is determined at a particular position, how can one determine the direction of change. In other words, is there any way to determine if methylation is increased or decreased?