Dear colleagues,

I'm planning a MBD-seq experiment to study if a toxic molecule affect genes methylation and I'm evaluating the possible approaches (and related bionformatic analyses needed).

Based on what have read I can go for the sequencing of the methylated fraction only or bot fractions (methylated and not-methylated). Considering the aim of the present study, I think that the first approach can be enough. However the second approach gives also an absolute estimate of methylation levels across genes (called gene specific MBD-scores).

Said that, how these MBD-scores are implemented in the bionformatic pipeline used to determine the differences between experimental groups? Are they actually used?

I get the point of these scores, but except of knowing the genes methylation level, which is the reason of calculating them if the goal is to find differences between groups?

Thank you in advance for your help!

Best

Marianna