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!
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