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hiruna72 / squigualiser

Visualise and analyse nanopore (ONT) raw signals
https://hiruna72.github.io/squigualiser/
MIT License
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Base-Wise alginment question #59

Closed xianyu0623 closed 3 months ago

xianyu0623 commented 3 months ago

Hi hiruna72! Thank you for proposing such a fantastic tool for nanopore raw data. I have some questions on how the tool implements base-wise alignment. I have read some papers about the raw data alignment, but they focus on kmer-event alignment. If I do not make it wrong, for a Kmer-event alignment pair, you align the event's signal to the middle base in a Kmer. Is it right? Thanks a lot for your help!

hiruna72 commented 3 months ago

Hi @xianyu0623,

Thanks for appreciating our work.

Yes, you are correct, we transform the kmer-to-signal alignment to a (most significant/influential) middle base-to-signal alignment.

You can find the middle base indices we have figured for different nanopore chemistry, pore model and base calling models. https://github.com/hiruna72/squigualiser/blob/main/docs/profiles.md#precomputed-forward-and-reverse-base-shift-values

For more details refer to our preprint (specially the sup note 3). https://www.biorxiv.org/content/10.1101/2024.02.19.581111v2

xianyu0623 commented 3 months ago

Thanks a lot for your timely answer!