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yupenghe / methylpy

WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
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DMR #77

Open liyangyang12 opened 2 years ago

liyangyang12 commented 2 years ago

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

yupenghe commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

Thanks a lot for your reply.