What is "sliding window"? I heard people use it to visualize the whole genome sequencing results (for example to show the spreads of mutation across the whole genome)
Very simply, you take a window of some size, 10, 100, 1000 base pairs. You can then answer some question about what happens in that window. How many mutation occur in this window, how many reads align to this window, etc. The you slide the window by moving the window by some number of basepaires. Normally the distance you slide will be less than the width of the window. So if your first window is chr1 basepair 1-100 your next window might be chr1 basepair 2-101 or 10-110.
Sliding windows are genomic intervals that literally "slide" across the genome, almost always by some constant distance.
These windows are mapped to files containing signal or annotations of interest, such as: SNPs, motif binding site calls, DNaseI tags, conservation scores, etc.
Once mapped, an operation or action is performed. For example, it can be interesting to scientists to count how many genomic annotations are within a sliding window, as that window moves across the genome. Or we might measure statistics of score data over windows, like the average or median conservation score, and so on.
Sliding windows can overlap or be disjoint. Overlapping windows are often used to "smooth" signal, to remove or reduce the impact of signal noise.
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