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Sequencing of mRNA from Whole Blood using Nanopore Sequencing
Published on: June 3, 2019
Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures
Hongxu Ding1,2, Ioannis Anastopoulos3,4, Andrew D Bailey3,4
1Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA, USA. hding16@ucsc.edu.
None:
The characteristic ionic currents of nucleotide kmers are commonly used in analyzing nanopore sequencing readouts. We present a graph convolutional network-based deep learning framework for predicting kmer characteristic ionic currents from corresponding chemical structures. We show such a framework can generalize the chemical information of the 5-methyl group from thymine to cytosine by correctly predicting 5-methylcytosine-containing DNA 6mers, thus shedding light on the de novo detection of nucleotide modifications.
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