Enhancer region

Question

[rheab1230]

I have Chip seq data for du145 cell lines I want to specifically look at enrichment of motifs in enhancer region. How do I separate enhancer from promoter region?

Answer 1

[xmLiu]

You can annotate the location of Chip-seq peaks in the genome use the R package ChIPseeker, or you can use bedtools to filter peaks overlapped with promoter.