Detection of DNA 5mC/6mA methylation by Oxford Nanopore sequencing data.



DNA base modifications, such as C5-methylcytosine (5mC) and N6-methyldeoxyadenosine (6mA), are important types of epigenetic regulations. Short-read bisulfite sequencing and long-read PacBio sequencing have inherent limitations to detect DNA modifications. Here, using raw electric signals of Oxford Nanopore long-read sequencing data, we design DeepMod, a bidirectional recurrent neural network (RNN) with long short-term memory (LSTM) to detect DNA modifications. DeepMod has been evaluated on several E. coli Nanopore data, two human Nanopore data and one algae Nanopore data with two common types of modifications: 5mC and 6mA. For 5mC detection, DeepMod achieves average precision up to 0.99 for both synthetically introduced and naturally occurring modifications. For 6mA detection, DeepMod achieves ~0.9 average precision on Escherichia coli data, and have improved performance than existing methods on Chlamydomonas reinhardtii data. In conclusion, DeepMod performs well for genome-scale detection of DNA modifications and will facilitate epigenetic analysis on diverse species.


The flowchart of DeepMod.






DeepMod is publicly available at


Liu Q, Fang L, Yu G, Wang D, Xiao CL, Wang K. Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data. 2019