how to add bed files together

Question

[dimitrischat]

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

[GenoMax]

You don't want to open them independently?

Please edit the title of the post so it matches the question.

[dimitrischat]

maybe i can make some sense now..

[GenoMax]

Ok. So post the command you are trying with bedtools merge that gives no output.

[GenoMax]

You need bedtools intersectbed (rather than merge). Take a look at the documentation for intersectbed here.

[dimitrischat]

i cant seem to find the command for this.

[GenoMax]

What do you mean by that? The linked help page has many ways of how to use intersectbed program.

intersectBed [OPTIONS] -a <FILE> \
                       -b <FILE1, FILE2, ..., FILEN>

[msimmer92]

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?

[GenoMax]

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.

[msimmer92]

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

[dimitrischat]

mergeBed a.bed o.bed -i > all.bed

Answer 1

[Alex Reynolds]

If you have an arbitrary number of files you want to generate the union from, use BEDOPS bedops -u:

$ bedops -u A.bed B.bed ... N.bed > answer.bed

If you have an arbitrary number of files whose intervals you want to merge, instead use BEDOPS bedops -m:

$ bedops -m A.bed B.bed ... N.bed > answer.bed

Merging creates new intervals from overlaps between input intervals. Unioning creates a larger set from all the input intervals, but doesn't otherwise modify them. You would pick one of the other operation depending on what you're trying to do.

[dimitrischat]

thanks a lot!! but i wonder why mergebed doesnt work..

[Alex Reynolds]

No idea. But BEDOPS tools are often worth trying.

[GenoMax]

mergebed is designed for only one bed input.

[msimmer92]

This works wonderful, thank you. Just out of curiosity, is there an analogous of bedops -u in bedtools? (before someone answers bedtools intersect or merge, make sure that the options you include actually make the same output as bedops -u, because the default does not...please be more specific)

Answer 2

[shahramsaghaei85]

Simply by 'cat'

$ cat file1.bed file2.bed fileN.bed > concat.bed

In order to sort them use 'bedtools'

$ bedtools sort -k1,1 -k2,2n in.bed > in.sorted.bed

Then if you need to merge overlaps, use bedtools merge