I am confused about sliding window method, we often using this method to analysis ChIP-seq data or Copy number variation(CNV).
Sliding windows w/o overlap is divided genome into several equal segments, it often used in CNV analysis. Sliding windows w/ overlap is like moving average in statistics.
I read the thread Question: Sliding Window for CNV Analysis, but it doesn't compare those two methods. Is sliding windows with overlap better than sliding window without overlap? Should we using sliding window with overlap on ChIP-seq data analysis?