Multi_read Fast5s - Githubissues

bioinfomaticsCSU / deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads

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Multi_read Fast5s #19

Open vahidAK opened 5 years ago

vahidAK commented 5 years ago

Hi, Is there any possibility that you update DeepSignal to accepts multi-read fast5 files? Because, when the number of samples is high, it is painful to convert multi-read files to single read and produce hundreds of millions of files. Thanks, Vahid.

PengNi commented 5 years ago

Hi @vahidAK ,

Thanks for your interest. We are already working on it. However it could take months. Because deepsignal depends on tombo to preprocess the fast5 files. And tombo doesn't support multi-read fast5 files either.

We are considering to wrap the core code of tombo into deepsignal. I'll let you know when we finish the upgrade.

Best, Peng

vahidAK commented 5 years ago

Hi @PengNi , Thanks for your kind response. I am looking forward to hearing about the new update.