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hiruna72 / squigualiser

Visualise and analyse nanopore (ONT) raw signals
https://hiruna72.github.io/squigualiser/
MIT License
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squigualiser realign gives only multiples of stride(=5) in the original model #44

Closed Marjan-Hosseini closed 9 months ago

Marjan-Hosseini commented 9 months ago

I am trying to use squigualiser realign to re-squiggle the move table generated by Dorado, using the following command:

squigualiser realign -p reform_output.paf -b sorted_t2t.bam -c -o realigned.paf

It gives me a move table similar to: image

The problem is that moves seems to be all multiples of 5. Is there a way I can get a move table values that are not multiples of 5?

hasindu2008 commented 9 months ago

Move tables from Guppy or Dorado are always a multiple of a stride size. You can use the f5c eventalign method which provides alignments that are not multiples of any number.

hiruna72 commented 9 months ago

@Marjan-Hosseini squigualiser's realign tool does not refine boundaries. Please use f5c eventalign. Also have a look at these documents. https://github.com/hiruna72/squigualiser/blob/main/docs/different_alignments.md https://github.com/hiruna72/squigualiser/blob/main/docs/RNA_visualisation.md

hiruna72 commented 9 months ago

Hello @Marjan-Hosseini,

I will close this issue now. Feel free to open again if you face related problems.