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Fig. 4 | Genome Biology

Fig. 4

From: NucHMM: a method for quantitative modeling of nucleosome organization identifying functional nucleosome states distinctly associated with splicing potentiality

Fig. 4

Nucleosome positioning of each of HMM states. A The illustration of nucleosome positioning definition and reference positioning score calculation. The upper panel showed the definition of well-positioned as well as fuzzy nucleosome. The bottom panel schematically drew the elements that were used to calculate the reference nucleosome positioning: width at half height restricted by fitted boundary, the number of reads and the variance of the reads centered by the identified dyad. B The correlation between each iNPS-derived positioning equation and reference positioning score equation in MCF7 cell type. Equation 8 showed the best correlation with the reference positioning score. C The violin plots showed the distribution of the nucleosome positioning score of each HMM states. D IGV visualized the nucleosome reads distribution and the positioning score calculated by Eq. 8. Green box shows the well-positioned nucleosome with a high positioning score, and red box shows the fuzzy nucleosome with a low positioning score

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Genome Biology

ISSN: 1474-760X

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