Extract all genes within 5 kb, 10 kb of a genomic range.

[demis001]

I have a genomic region that have chr, start and end as a bed format. I have a gene annotation in bed format too. What is the best way to extract all genes within 5 kb, 10 kb of a given genomic range from gene annotation bed file?

Chr1  125086657 125086787
ChrX  121333162  121334618

I was using bedtools closest to extract the nearest genes, but don't know how to achieve to extract all annotation within 10 kb.

[splaisan]

have a look to bedtools flank instead then bedtools intersect the result with your gene file (bed or even GFF does here)