Bed tools for comparing files and calculating the percentage of different parts

Question

[osiemen]

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!

[osiemen]

I think i made a mistake by saying that i wanted to use the combinations of these files as a whole. Since I think I should map my files against the whole human genome in order to say something about the chance that a mutations can occur in the files i use?

pls correct me if i am wrong!

[WouterDeCoster]

Well you can use bedtools merge to combine e.g. all TAD files and bedtools coverage to figure out the included lengths of the intervals. And you know the size of the human genome, so I guess you can then count the percentage. Or did I misunderstand?