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Nanopore sequencing can detect multiple base modifications simultaneously and we can leverage this capability by introducing exogenous base modifications at specific functional regions. One such method uses a 6mA methyltransferase such as EcoGII or Hia5 to label accessible regions of chromatinized DNA, usually by treatment of cell nuclei with the enzyme.
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Modkit comes with a machine learning model that has been trained to identify regions of open chromatin based on 6mA signal. You can invoke this model with the following command: