DMR analysis

[DayTimeMouse]

Hi,

Thanks for developing this nice tool.

I have already obtained the output of pb-CpG-tools for Normal and Tumor sample(no repeats), and now I'd like to compare CpG regions between Normal and Tumor, like DMR analysis. How can I use methBat to do this?

Best regards.

[holtjma]

Hi @DayTimeMouse,

We have a few different workflows described in our documents: https://github.com/PacificBiosciences/MethBat/blob/main/docs/user_guide.md#main-workflows

Depending on the number of datasets you have and the intended scope of methylation analyses, you may want to try different ones. Happy to answer any specific questions, but I'd suggest starting there and seeing if any of them match your desired outputs.

Matt