Hi all,
I have bisulfite-sequencing data for two plant species (biological triplicates), but only for one condition each. The research question was originally confined to one locus but now I would like to call differentially methylation regions between genomes.
I have synteny tables for both genomes. The question is wether you think it might be better to compare methylation in the syntelogs "by hand" or use some bioinformatics tool for that. All tools I found call methylation levels _per genome_ for different treatments, but they do not call differential methylation _between_ genomes. Another alternative would be to map the reads for both species against a third equidistant genome and handle the reads from both original species as treatments. I am curious on your takes on this problem.
Thanks a lot!
Sebastian
