Fig. 7: DeepRM precisely quantifies m6A modification stoichiometry across the transcriptome at various sequencing depths.

a The scatter plots of m⁶A modification stoichiometry in the HEK293T transcriptome quantified by GLORI (x-axis) and four Nanopore-based methods (DeepRM, Dorado, m6Anet, and SingleMod; y-axis). m⁶A modification stoichiometry of those sites with sequencing depths of > 40, 31–40, 21−30, 11–20, and 5–10 are shown (top to bottom). For depths of ≤ 20, the m6Anet result is not shown since m6Anet requires a minimum sequencing depth of 20. The color scale indicates Gaussian kernel-estimated density. Pearson’s R², Spearman’s ρ², and the number of samples are shown. b The scatter plots of m⁶A modification stoichiometry in the HeLa transcriptome quantified by eTAM-seq (x-axis) and the four Nanopore-based models (y-axis). Otherwise, as in (a).