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fanglab / nanodisco

nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nanopore sequencing.
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Could nanodisco detect methylation from other species #2

Closed lemonsky123 closed 3 years ago

lemonsky123 commented 4 years ago

HI, @fanggang @jbeaulaurier ,Could nanodisco detect methylation from other species, such as human?

touala commented 4 years ago

Hello @lemonsky123,

Thank you for your interest in our tool. nanodisco is currently focused on de novo discovering, typing and fine mapping methylation motifs, the key challenge that prevents broad use of nanopore sequencing for the de novo study of bacterial epigenomes. We do not recommend using nanodisco to look for methylation in human because 1) in the human genome, 5mC is mostly at CpG sites, for which multiple existing tools, such as Nanopolish and Tombo, have been specifically trained; 2) for 6mA/4mC, if they exists in the human genome, it is at much lower level than 5mC, and would probably require different strategies for detection. Please see Question-7 in the FAQ page for more information: https://nanodisco.readthedocs.io/en/latest/faq.html#q-methylation-event.

Feel free to reach back to us if you have other questions.

Alan

touala commented 3 years ago

I'll close this issue. Feel free to reach back to us if you have other questions.

Alan