For purposes of proposaling and reports, I have gone back to look at a small project done in collaboration with scientist at IFREMER looking at pesticide exposure on oyster larvae methylation.
The control library had limited yield so the number of loci with data from the treated and the control library was restricted. However using a liberal 3x coverage for both, we found a total of 823 DMRs (544 hypermethylated and 279 hypomethylated).
Intriguingly, when one accounts for all CGs in the genome, these DMRs are predominantly in transposable elements.
Reminiscent of …
The analysis is not pretty, but here is what I have to offer.
https://github.com/sr320/nb-2015/blob/master/Cg/YE-pesticide/YE-pesticide-summary.ipynb
Steven Roberts
fu- the direction of methylation in TEs in predominantly hypo, or loss of methylation.