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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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How to detect 6mA methylation using deepsignal? #8

Closed tianrenmao closed 5 years ago

tianrenmao commented 5 years ago

Can I detect both 5mC and 6mA methylation with the model provided?

PengNi commented 5 years ago

Hi @tianrenmao ,

To detect 6mA, a new model must be used. One model is supposed to predict the methylation state of one targeted motif in DeepSignal.

We didn't provide the 6mA (GATC) model used in our published paper, because it doesn't have a stable performance for other organisms (except the plasmid).

You can try to train a new model for 6mA by using features of a certain targeted motif.

Best, Peng

SAMtoBAM commented 3 years ago

Hello Is the model provided in the google drive "model.GATC.R9_2D.tem.puc19.bn17.sn360.tar.gz" suitable? Thank you

PengNi commented 3 years ago

@SAMtoBAM , as the 6mA model is trained using R9 2D reads and only suitable for GATC motif, it is not suitable for any further use now.

Best, Peng

SAMtoBAM commented 3 years ago

Hi @PengNi, Will/Can you release a 6mA model now or in the future? Thank you

PengNi commented 3 years ago

Hi @SAMtoBAM ,

Thanks very much for your interest. However, now we don't plan to release a DNA 6mA model, as we don't have data to train a more accurate model.

Megalodon may be a good choice to detect DNA 6mA at present.

Best, Peng