I am struggling to find a way to calculate DMRs from MeDIP-seq data in Galaxy. I know there are plenty R based program to do this, however since I am a total R-noob I will be limited to galaxy.
We have 2 different seq samples from: control treated cells and cells treated with a cytokine. The idea is to know which regions in cytokine treated cells are enhanced related to the control cells.
I already acquired cytokine specific, control specific and overlapping regions using genomic overlaps. However as there is still a possibility that the overlapping regions are differentially methylated these will need to be calculated.
thanks in advance,