DMR

[liyangyang12]

Dear yupenghe,
Why DMR does not need to distinguish +/- strand like DMS ?
Thanks.

[yupenghe]

It is possible by running DMR finding twice on allc files with just + strand CpGs and a separate set with just - strand CpGs. The reason for DMRfinding combing +/- strand is that in almost all cases, differential methylation on a specific occurs in both strands.

[liyangyang12]

Thanks a lot for your reply.
If I want to calculate the DNA methylation level in the promotor region of + stand genes using methylpy add-methylation-level, do I need to think about +/- strand?
The CpG methylation levels of the +/- strands of the almost entire genome are similar, right?
Thanks.

[yupenghe]

If I want to calculate the DNA methylation level in the promotor region of + stand genes using methylpy add-methylation-level, do I need to think about +/- strand?

In generally no because the interaction between transcription factors and DNA methylation is not strand specific.

The CpG methylation levels of the +/- strands of the almost entire genome are similar, right?

Yes. That is another major reason.

[liyangyang12]

Thanks a lot for your reply.