Genome windows and counts

Each chromosome is cut from position 0 into windows of the chosen size, and the last window stops at the chromosome end; a step smaller than the window gives overlapping sliding windows.

With intervals to count, each window gets the number of overlapping intervals, bases covered, window length and fraction covered; the line chart shows counts along the genome to reveal regions rich in variants or peaks.

With “each BED region”, windows are made inside every region (for example fixed-length pieces along gene bodies).

Window coordinates follow the BED convention (0-based start, end not included) and can go straight into other interval tools.

Method

Window rules match BEDTools makewindows (-w/-s/-i), and counting equals intersect -c / coverage (Quinlan & Hall 2010, Bioinformatics 26:841), checked line by line on the same inputs.

Data size

Up to 500,000 windows; runs in your browser.