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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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Results of extract features step #49

Closed Jerry-0591 closed 3 years ago

Jerry-0591 commented 3 years ago

Hi, I am now trying to reproduce your example. According to your guidance, at the extract features step, the output file will be a tab-delimited text file. And I am confused with two terms of this file, "strand" and "read_strand", what is the difference between them? For my trying, the "read_strand" is all t in the output file, is it something that I missed?

PengNi commented 3 years ago

Hi @zcWang0591, read_strand is a legacy feature for R9 2D reads. An R9 2D read has a template sequence and a complement sequence. However R9 2D technique is no longer used by Nanopore. 1D reads only have a sequence in template strand.

Best, Peng

Jerry-0591 commented 3 years ago

Thank you! It is clear now.

Jerry-0591 commented 3 years ago

Hi, I still have a little problem that if I want to train a model for my experiment data, the features extracted by Deepsignal include read_strand, which is designed for R9 2D technique, but my experiment uses 1D technique, so does it influence the downstream process? Or I just ignore it？

PengNi commented 3 years ago

@zcWang0591 ，yes, you can just ignore it.

Jerry-0591 commented 3 years ago

OK, thank you