Fig. 4

The SCRMshaw-HD protocol. The new, more robust SCRMshaw-HD protocol is shown to the left, with the default SCRMshaw protocol to the right. a In both protocols, 500 bp windows are scored with a 250 bp offset between windows. b, c For SCRMshaw-HD, this process is parallelized by running 25 instances of SCRMshaw simultaneously, with each instance starting its first window at a different starting points corresponding to 0, 10, 20, 30, …, 240 bp from each chromosome/scaffold end. d The output from the individual SCRMshaw runs is concatenated into a single output representing 500 bp windows with 10 bp offsets across the entire genome. e The SCRMshaw scores for each 10 bp genomic window are summed, with any individual score (orange boxes) below the value of the 5000th ranked score reassigned to zero (gray boxes). The summed scores (f) are used as the basis for peak calling. Any peaks with amplitude above the selected amplitude threshold (g, red dot) are then evaluated for SCRMshaw score (h, red dot; see Methods for details). Peaks meeting both criteria (e.g., peak “d” in panel f) are accepted as “top predictions.” Peaks that either fall below the amplitude cutoff (e.g. “b” in panel f), or which pass the amplitude cutoff but not the score cutoff (“a” in panel f) are not considered top predictions. In default SCRMshaw (right side of figure), those predictions with SCRMshaw score above the elbow point of the curve of all ranked SCRMshaw scores are considered to be “top” predictions (h, red dot)