How to calculate the input-subtract signal for a specific enhancer region

Question

[biofandd]

Hi,all. I'm a tiro for ChIP-Seq, Now, I want to compare ChIP-Seq signal between two conditions, and therefore I plan to calculate the input-subtracted signal for each enhancer region to yield reads per kilobase per million (RPKM). How to get the RPKM info based on the bed file of enhancer peaks and signal bigwig?