How would I find the intergenic regions on a bed file using an awk script and separating the strands by + and -?
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:
Does this take care of overlapping genes?
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