How to know the genome coordinate of DNaseI hypersensitive sites large peaks?

Question

[bright602]

Hi there, could anyone tell me how to know the genome coordinate of DHS sites complete peak? One problem I came across on the bed file is that the genome coordinate just shows small regions (approximate 150 bps) instead of showing the large peaks. Thanks and looking forward to the reply.

Answer 1

[John Torcivia]

Do you have the raw data or is the only data you have this bed file? Are these small regions adjacent to each other? It's possible that each small region has a certain signal, and multiple small regions together are showing the full broad peak (which could have a variety of different signal strength, not just uniform across the entire area). If you have the raw data or alignments you could use something like MACS to generate a narrow or broadpeak file.