I have multiple BED files and I know that for each file some of the intervals are shared with some of the other files, while some are unique (for example present in one or 2 files only).
Ideally, the final table should contain all the possible intervals with 2 columns, one for the count of frequency of occurence (for example, found in 4 files) and one with the names of the files in which that interval has been found.
What's the best way to do this?
I was thinking:
Merge all the BED files, and then
Use bedtools coverage to intersect the files one by one with the merged file but I have no idea how to make the plot the output.
I imagine this will require some scripting in perl but this is entirely new to me and I could really use some help...
Thank you in advance!