Hi I know that there must be way to do this with bed tools, but i don't know exactly what to use from bed tools to do this. So please help be out :)
I have multiple bed files for promoter, enhancer and TAD locations. I use these files for annotation and i want to to calculate the chance that a mutation occurs inside a promoter, enhancer or a TAD since these files are of different sizes. I have more enhancer and TAD bed files so the chance i find a SNV in these regions is bigger. So basically i want to calculate first the overall size (=coverage??) of the files together and then calculate the percentage for certain parts. --> part departed by whole , promotor / (whole = TAD+promoter+enhancer) * 100
I hope I am clear enough!