Hello all,
I’m working on a mouse study where I’ve merged cancer and control samples, and I’d like to perform a paired DMR analysis using modkit.
To do this, I need a BED file in the correct format for modkit. So far, I’ve tried creating bins (e.g. 300 bp or 5000 bp windows), but these are essentially random regions and don’t give me much biological insight. What I’d really like is to focus on specific features such as promoter regions or CpG islands, so that I can interpret the results more meaningfully.
A few questions I’m hoping the community might help with:
Is there a publicly available mm39 BED file with promoters or CpG islands that is compatible with modkit?
Given that my data has very low coverage, is running a paired DMR analysis likely to be informative, or am I wasting effort at this stage?
Is my current approach (fixed-size bins) reasonable for exploratory analysis, or would you recommend starting directly with annotated regions?
Any advice or pointers would be very much appreciated!
Best, Felix
