obtain non-overlapping regions within the file
Hi
I have a file like this
chr1 1 100
chr1 1 50
chr1 55 70
chr1 75 100
chr1 101 200
I want to obtain all non-overlapping regions into separate file. So my output will look like this
chr1 1 100
chr1 101 200
Is there any way to do this please let me know
• 3,774 views
•
link
updated
by
dariober
•
written
by
ancient_learner
•
written
by
ancient_learner
2 answers
With BEDOPS bedops and sort-bed:
$ sort-bed input.bed | bedops --merge - > answer.bed
Sorting is required to deal with matches in the second (start position) column. Make sure your input BED file is tab-delimited.
• 2 views
•
link
written
by
Alex Reynolds
Log in to answer this question.
More posts like this
-
partition single bed file into non-overlapping regions
written by jrose •
-
Genome coverage within specified regions
written by ilovesuperheroes1993 •
-
how extract our desirable data from two table?
written by star
-
How to report genomic intervals essentailly overlapping in all files?
written by lakhujanivijay
-
Find consensus overlap between many bed files
written by goodez
-
How to merge chr+strand+coordinate+score from multiple files?
written by Rae •
-
bedtools what in B absent from A
written by Medhat
-
Split bed file by unique first three columns
written by graeme.thorn
-
how to merge overlapping intervals in a bedgraph file
written by Fidel
-
Identify reads overlapping a junction in gff file
written by jkhurana2311 •
This was already answered here