thanks a lot!! but i wonder why mergebed doesnt work..
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dimitrischat
how to add bed files together
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
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Alex Reynolds
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dimitrischat
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dimitrischat
3 answers
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.
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Alex Reynolds
No idea. But BEDOPS tools are often worth trying.
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Alex Reynolds
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)
mergeBed a.bed o.bed -i > all.bed
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dimitrischat
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
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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.
mergeBed a.bed o.bed -i > all.bed
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