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nanoporetech / flappie

Flip-flop basecaller for Oxford Nanopore reads
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kmer model #47

Open joshidhaivat opened 4 years ago

joshidhaivat commented 4 years ago

Hi,

It suggests that flappie has separate models (r941_native and r941mC_native) for R9.4 MinION and PromethION flow cell. Can you please let me know if there is a way to extract the kmer model from this (with the mean and standard deviation of the current values corresponding to each kmer)?

Thank you, Dhaivat

tmassingham-ont commented 4 years ago

Hello. The "flip-flop" model in used in Flappie has no notion of a kmer, so I'm afraid this isn't possible.

An alternative would be to use the squiggle models in the Scrappie project (see scrappie squiggle command), which give a mean and standard deviation for each position in a sequence.