If genomic DNA had polyA tracts that you wanted to (very roughly, maybe to within ~10 bp?) know the length of, would this model be useful? How good is the normal (but low coverage) nanopore / nanopolish pipeline at estimating the lengths of polyA > 5 bp?
New nanopolish release (0.10.2) containing the first public version of our poly-A tail length estimator for direct RNA reads: https://github.com/jts/nanopolish#release-notes …. Developed by Paul Tang in my group.
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this code is specific to direct RNA poly-A tails but you could do something similar for DNA homopolymers. Might be worth writing a general-purpose caller
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Awesome! Congrats guys, great effort. Does Paul not have a twitter ?!?
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he's working on it...
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This looks very interesting. Is there a description of the model available, or in the works? I see from the code something to do with a HMM, but couldn't really understand it.
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We'll have a full description in an upcoming preprint. The short version is that we use an HMM to segment the signal and estimate the duration of the poly-A signal, then convert that to an estimated length.
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