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smaegol / nanotail

R package for visualization and exploratory analysis of Oxford Nanopore direct RNA seq based polyA predictions
GNU General Public License v3.0
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Dwell time! #2

Closed g-s-2018 closed 1 year ago

g-s-2018 commented 2 years ago

Hi,

I am wondering how nanotail calculate the dwell time in Polya_data table?

Thanks in advance,

smaegol commented 2 years ago

Hi,

dwell time is in fact the number of sampling points for the poly(A) tail in the signal. To convert it to the actual time it should be divided by the sampling rate which for RNA should be 3012.

This is calculated as difference between nanopolish-calculated transcript_start and polya_start https://github.com/smaegol/nanotail/blob/79eb40c1bd666becb47a119cbf970769f04511c5/R/read_polyA_data.R#L34

I use this just for the comparison to calculated poly(A) length.

I hope it helps