Enrichment of peaks genome wide

[jeni]

Hi all,

I need help for enrichment estimation. I have a set of peaks (bed file) and I have already annotated them to promoter, exon, intron, intergenic regions. Now I want to check the probability of occurrence of peaks in each of the gene regulatory regions genome wide by using enrichment analysis. So, is there any tool available for this?

Thanks.

[dariober]

There are quite a few options. See this thread on biostars
Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. genome average)
Personally I quite like GAT