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jmschrei / PyPore

Tools used to analyze data from nanopore-based experiments.
http://jmschrei.github.io/PyPore/
MIT License
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How do bases and segments correspond one to one? #1

Open N-damo opened 3 years ago

jmschrei commented 3 years ago

I'm not sure what you mean. A segment, which I think is now commonly referred to as an "event" in the literature, is a slice of signal that exhibits steady statistical parameters. In theory, each segment should correspond to a change of one nucleotide in the pore.

N-damo commented 3 years ago

A nanopore can hold k nucleotides (k-mer) simultaneously. For example, k equals 5 for the pore version R9.4. Thus, the current changes indicate the k-mers that pass through the nanopores. I'm not sure whether each segment correspond to one nucleotide here.

jmschrei commented 3 years ago

Yes, in theory a segment should correspond to one nucleotide change in the pore. In this library, it's just a way to store a chunk of signal with stationary statistical properties. Whether the segments actually correspond to changes in the pore depends on the quality of the segmentation algorithm.

N-damo commented 3 years ago

everything is amazing. In the supervised machine learning, back to the very beginning, people how to know raw signal correspond to a real sequence.