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bioinfomaticsCSU / deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads
GNU General Public License v3.0
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No output with DeepSignal Extract Command #85

Open kewei2019 opened 1 year ago

kewei2019 commented 1 year ago

Hi,

I am writing to seek assistance regarding an issue I encountered while using DeepSignal for m6A methylation calling on the E. coli genome. The tombo processes yielded satisfactory results, indicating that the initial steps were successful. However, I faced difficulties when attempting to utilize the "deepsignal extract" command, as it did not produce any output. Any insights or recommendations you can provide would be invaluable in resolving this matter. Thank you very much for your attention and support.

Kewei Xu

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PengNi commented 1 year ago

Hi Kewei,

Thank you for trying deepsginal. However, the m6A model of deepsignal is for ONT R9 2D reads. It is too old and not compaitbale with modern ONT reads. For m6A detection I suggest using other tools.

Best, Peng

Moretta1 commented 4 months ago

hi,

I have come across the same question, I'm using 5mC dataset as well, but it gave empty output in the extract step and the same as the output above.