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PengNi / deepsignal-plant

Detecting methylation using signal-level features from Nanopore sequencing reads of plants
GNU General Public License v3.0
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Using updated nanopore flowcells for Arabidopsis ? #20

Open JBerthelier opened 2 years ago

JBerthelier commented 2 years ago

Dear DeepSignal authors,

Thanks for this great tool !

I was wondering if we can use R10.4 flowcell or is it better to use R9.4 for Arabidopsis methylation calling ? (I was using R9.4)

I see that the trained model was obtained with R9.4 .

Best regards,

Jeremy

PengNi commented 2 years ago

Hi Jeremy,

Thank you for your interest of our tool! Currently the trained model is only compatible with R9.4 data. We now don't have a model for R10.4 flowcell, because we haven't got any R10.4 reads that can be used for training yet.

Best, Peng

JBerthelier commented 2 years ago

Dear Peng,

Thanks for the quick answer. We will got R10.4 reads for A. thaliana. If you are interested I can keep you posted if we choose to train those data.

Best ,

Jeremy

yusmiatiliau commented 1 year ago

Hello DeepSignal-Plant Authors,

Following up on this thread, I wonder if there is a plan in the near future to include R10 models? We have some grapevine sequencing data, that we would like to call methylation from. Thank you,

PengNi commented 1 year ago

Hi @yusmiatiliau , thank you very much for your interest of our tool. I want to, but we don't have a plan in the near future to include R10 models. We don't have any R10 data yet. Maybe in the future we will have a R10 model, but not in the near future.

Best regards, Peng

PengNi commented 5 months ago

@yusmiatiliau , @JBerthelier , Hi all, very sorry for the delay! Our tool deepsignal3 supports R10.4.1 POD5 format now. Please check the deepsignal3 repo for more details if you are still interested.

Best, Peng