Subtracting bed file from whole genome

Question

[arsala521]

Hi,

I have a list of hg38 genomic regions in a bed file. I want to subtract these regions from whole genome sequence and get resultant regions in another bed file. What would be the appropriate way to do that? What I thought was to create whole genome bed file based on hg38.chroms.sizes file and then use bedtools subtract, but I was wondering if there could be some other appropriate way?

Thank you

Answer 1

[ATpoint]

Make a BED file for the genome, so chromosome name and as coordinates 0 as start and the chromosome length as end. Then use bedtools complement to ‚subtract‘ your regiome from the genome.