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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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Using multiple fast5 dirs #66

Closed unnatisonawala closed 3 years ago

unnatisonawala commented 3 years ago

Hello,

I have two single fast5 directories (from two Nanopore runs for the same sample) that I have resquiggled using Tombo in the past. Is it possible to give deepsignal two dirs to call modifications from? I ask since the Tombo index files are separate for each of the directories, so in order to merge them I would have to run resquiggle again if I understand correctly.

Thank you.

PengNi commented 3 years ago

Hi @u2progress , deepsignal doesn't support multi dirs as input at present. deepsignal doesn't need tombo index files either. So you can call the two dirs seperately, without resquiggle them again.

Best, Peng

unnatisonawala commented 3 years ago

Thanks for your swift reply @PengNi ! Since these runs are for the same genome and sample, I wanted to get modifications utilising the entire dataset and coverage. If tombo index isn't required, I could move the two fast5 dirs into a single one for the purpose of running deepsignal since it searches recursively. Is that right?

PengNi commented 3 years ago

Yes, the two dirs can be moved into one.

Best, Peng

unnatisonawala commented 3 years ago

Perfect, thank you again.