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Psy-Fer / deeplexicon

Signal based nanopore RNA demultiplexing with convolutional neural networks
https://psy-fer.github.io/deeplexicon/
MIT License
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Will resnet20-final work for SQK-RNA004? #26

Closed hugofriedrich closed 1 year ago

hugofriedrich commented 1 year ago

Dear Psy-Fer,

thanks a lot for this method, it has been really useful!

We were wondering if the model (resnet20-final.h5) you trained to multiplex the reads would work on fast5 files generated by the new dRNA flow cell chemistry released by ONT this fall (2023) SQK-RNA004.

Best! Friedrich

Psy-Fer commented 1 year ago

Hey there,

Probably not. Apparently ONT are working on barcoding internally and we would need access to RNA004 to be able to create training sets for this (which we don't have access to yet).

If there is a very large gap between ont providing barcoding for RNA004 and its general release, I might consider making a new and improved version of deeplexicon, but without that information, it's a fair amount of work to then be made redundant* by ont. (see slow5/pod5 mess, and we had a much larger lead on that😅)

James

hugofriedrich commented 1 year ago

Hey James,

thanks a lot for the swift response! I guess we will wait and see then.

Best, Friedrich