how to compare methylomes

[dnusol]

Hi, I am new to bisulfite sequencing and am confronted with an experiment where I would have to compare methylation states for several samples, some of which are paired (i.e. same individual, different tissues).
After some reading I have found Bismark to do methylation analysis on a one-by-one sample basis, if I am not wrong. I think I will be using Bismark for detecting methylation in a per sample basis.

But my question is, can anyone provide some guidelines as to how to compare samples after detecting methylation hotspots and if it is possible to take into account the pairing issue? Also, any references I can look for would be great.

Thanks

Dave

[dnusol]

In case it helps anyone, I found this article with one possible solution:

Bioinformatics. 2013 May 8.
Detection of Significantly Differentially Methylated Regions in Targeted Bisulfite Sequencing Data.
Hebestreit K, Dugas M, Klein HU.