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hyeshik / poreplex

A versatile sequenced read processor for nanopore direct RNA sequencing
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how to get polya length in nts? #15

Closed Huanle closed 5 years ago

Huanle commented 5 years ago

Hi Hyeshik, How to convert polya squiggles into length measured in nucleotides? polya squiggle length / full squiggle length (duration) * sequence length ? What is polya_dwell in the summary file? Time taken to sequence polyA? Thanks a lot.

hyeshik commented 5 years ago

Hi Huanle, We're still in studying the relationship between the physical length of a poly(A) tail and the dwell time migrating through a nanopore. What we can sure at this stage yet is that the relationship is hard to model with a simple linear function with one or two coefficients calculated from the neighboring signals. I guess I would be able to add poly(A) length in nt after exploring the measurements from several trials of poly(A) standards. Still, the bare poly(A) dwell time can be a good statistic when comparing between samples sequenced together in parallel.

Huanle commented 5 years ago

Thanks @hyeshik . I look forward to the update on polya length reported in nts. :)

Huanle commented 4 years ago

Hi @hyeshik , Is there any progress on this specific topic? Thanks.