How to extract intergenic regions

Question

[Ak]

I'm trying to obtain intergenic regions from the fasta file containing the genome sequence.

I previously identified the exon-intron boundaries of a gene family (using TopHat) and obtained a bam file containing the exons, and a bed file containing the intervals. So now I'm trying to extract the intergenic regions of this gene family with the hope that I can fully utilize these files.

Hope that anyone would have any suggestion.

Thanks!