Question: Merge overlapped gene coordinates in bed file format
0
gravatar for mkh
17 months ago by
mkh40
USA/CT
mkh40 wrote:

Hi

I have a bed format file which looks like this:

geneid start stop

geneA 100 250

geneA 120 320

geneA 240 600

geneB 1100 1800

geneB 1110 1600

geneB 1500 1700

and I would like to merge the overlapping intervals as follow:

geneid start stop

geneA 100 600

geneB 1100 1800

Are there any tools which I can use to merge such a file format?

Thanks

chip-seq • 340 views
ADD COMMENTlink modified 17 months ago by Pierre Lindenbaum130k • written 17 months ago by mkh40
1
gravatar for Pierre Lindenbaum
17 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum130k wrote:

bedtools merge https://bedtools.readthedocs.io/en/latest/content/tools/merge.html

ADD COMMENTlink written 17 months ago by Pierre Lindenbaum130k
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