search

bioinfomaticsCSU / deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads
GNU General Public License v3.0
109 stars 21 forks source link

Feature extraction #35

Closed vahidAK closed 4 years ago

vahidAK commented 4 years ago

Hi @PengNi Do you consider mismatches with the reference during feature extraction? As you know, the error rate of the nanopore is high and there may be many cytosines that actually might not be C when compare it to reference. I was wondering that deepsignal extracts features for cytosines that are called C from nanopore and also are C in the ref?

Thanks, Vahid.

PengNi commented 4 years ago

@vahidAK , we don't consider mismatches. We use Tombo for the resquiggle, which mapping the raw signals to the genome reference, after the read-genome alignment.