Marcus Stoiber

You have to match both marginal distributions in your simulation. Could you also sample from the percent methylated distribution? This will give a good indication if there is a linked...

Megalodon is being deprecated so I would recommend using Guppy, Bonito or Dorado. Megalodon has not been tested with the modified base guppy models so it may be an issue...

> is it appropriate to use the same thresholds? It is often a good idea to use the same thresholds for a larger experiment, especially when the estimated thresholds are...

Thanks for your questions! Here are some clarifications: 1. Discrepancy in row counts: Can you confirm how you counted the number of h rows? The total number of rows in...

Tombo is deprecated. I would highly recommend moving your pipeline to the Remora signal analysis API.

The core question here is what biological question are you trying answer? Can you compute percent methylation as `(Nmod / Nmod + Ncanonical + Ndiff + Nnocall)`? Absolutely! The fields...

There are several options for signal normalization that are set through the signal mapping refinement object. Depending on these settings several signal normalization methods may be applied. The default is...

The notebooks section of the repository contains details of how to apply sequence to signal alignment (re-squiggle). If there are some details missing there please describe them in more detail...

Presumably storing the resquiggle results is not the final goal. Remora has specifically removed any specified output format for sequence to signal mappings. The idea here is that resquiggle results...

I would suggest that you move your analyses over to Remora which can also perform per-read signal level analyses from standard nanopore data processing (POD5 and BAM). See the notebooks...