i have many bed files and i want to add them all together into one. ( so i watch it in igv ). any help ?
edit: i have found common areas and i want to have them in 1 bed file. bedtools merge or mergeBed doesnt seem to work. maybe my command is wrong. Also when i type mrgeBed or bedtools merge ( like when you type intersectBed and it prints out help/options) , it doesnt do anything. it seems to keep doing something. Version of my bedtools is 2.26.0
You don't want to open them independently?
Please edit the title of the post so it matches the question.
maybe i can make some sense now..
Ok. So post the command you are trying with bedtools merge that gives no output.
You need
bedtools intersectbed
(rather than merge). Take a look at the documentation for intersectbed here.i cant seem to find the command for this.
What do you mean by that? The linked help page has many ways of how to use intersectbed program.
Since we are discussing the bedtools intersect command: Is there a flag or something to add to bedtools intersect get the union, if I wanted to get it?
Original question has this requirement:
edit: i have found common areas and i want to have them in 1 bed file.
It was not asking for union.Yes, you are right, you answered the users question properly because that question suggest finding the overlap. I just wanted to know for the union case and got confused reading the other answer. Let me rephrase
mergeBed a.bed o.bed -i > all.bed