Appear negative value while caculating Input-subtract signal for ChIP-Seq

Question

[biofandd]

For a region, the signal in treat sample is 0, but have signal in Input-background. Therefore, It will appear negative value while caculating Input-subtract signal. How to do with this situation?

[Bastien Hervé]

I use to set those regions to 0 in my ChipSeq analysis, as you can not have less than nothing