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Models developed using Nanopore direct RNA sequencing data from in vitro synthetic RNA with all adenosine replaced by  N  6 -methyladenosine (m 6 A) are likely distorted due to superimposed signals from saturated m 6 A residues. Here, we develop a neural network,  DENA , for m 6 A quantification using the sequencing data of in vivo transcripts from Arabidopsis. DENA identifies 90% of miCLIP-detected m 6 A sites in Arabidopsis and obtains modification rates in human consistent to those found by  SCARLET , demonstrating its robustness across species. We sequence the transcriptome of two additional m 6 A-deficient Arabidopsis,  mtb  and  fip37-4 , using Nanopore and evaluate their single-nucleotide m 6 A profiles using  DENA .

genome biology

DENA: training an authentic neural network model using Nanopore sequencing data of Arabidopsis transcripts for detection and quantification of N6-methyladenosine on RNA