Hello,

Thanks for the hipchipper tool! I have a conceptual question about how the anchors of interactions are identified in hichipper: from my understanding this is done by taking the peaks from Chip-seq data and then padding the region around these peaks taking into account restriction sites. I am interested in enhancer-promoter interactions, and my corresponding HiChip data uses H3K27ac which is an enhancer marker. However, if hichipper only identified interactions between anchors that include a H3K27ac peak, will it preferentially find enhancers-enhancer interactions? To enrich for enhancer-promoter interactions, would I somehow want to enrich for H3K27ac peaks in only one anchor per interaction?

Any help in understanding this concept around identifying interactions anchors is very welcome!

Many thanks,
Eva