Question: Finding intergenic regions in bed file?
0
gravatar for pavep
3.4 years ago by
pavep0
pavep0 wrote:

How would I find the intergenic regions on a bed file using an awk script and separating the strands by + and -?

awk • 2.2k views
ADD COMMENTlink modified 3.4 years ago by novice950 • written 3.4 years ago by pavep0
6
gravatar for novice
3.4 years ago by
novice950
United States
novice950 wrote:

1) You need to know the size of each chromosome to find all intergenic regions.
2) Do you have to limit yourself to awk? It is smarter to make use of available tools, like BEDTools:

bedtools complement -i genes.bed -g genome.txt > intergenic.bed

where genome.txt looks something like this:

chr1    249250621
chr2    243199373
...
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by novice950

Does this take care of overlapping genes?

ADD REPLYlink written 21 months ago by rsafavi50
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