Finding intergenic regions in bed file?
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5.1 years ago
pavep • 0

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

awk • 3.3k views
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5.1 years ago
novice ★ 1.0k

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
...
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Does this take care of overlapping genes?

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