Fig. 4
From: Exploring the relationship between intron retention and chromatin accessibility in plants
HMM footprint detection. The hexamer CCGCCG was detected to have a footprint at the location of the hexamer (red bar) in the standardized DNase I-seq data profile in both arabidopsis (a) and rice (b). The number of occurrences of the hexamer in IR/IE events is shown next to the k-mer in the title of each sub-figure. The profile extends 100bp upstream and downstream of the hexamer location, and is used by our HMM to score the k-mer for a potential footprint. In both cases, we see a clear dip in coverage indicating a possible footprint at the hexamer location