How to merge and compare multiple bed files containg some overlaps?

Question

[JustinZhang]

I got about 50 bed files from different sources, they are all well-formatted, and contains regions of hg19.

My question is: How to merge them and mark every new region with the times it appears in those files and names of them?

My expected output:

 #Chr    Start    End    Frequency    SourceFiles
 Chr1    123456    567891  8/50    1.bed,2.bed,3.bed...

or

#Chr    Start    End    Frequency    1.bed    2.bed    3.bed  ...    50.bed
Chr1    123456    567891  8/50    y    n    n   ....    y

I've tried Bedtools but the output is not what i want. Any practical ways to this?

Answer 1

[Pierre Lindenbaum]

try bedtools multiinter

[JustinZhang]

Much thanks!

To beginners like me, please understand the difference among bedtools Multiinter (Now called multiIntersectBed) , bedtools merge and bedtools genomecov first.

And never write a de-novo shell/py/perl script before searching and asking enough, because most of our questions have surely been posed and figured out by others.