Can Remora generate visualizations of the raw signal in a manner similar to the signal-to-reference mode of squigualiser?
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Hi ONT developer,
I have a small question about how to use Remora.
Can I use remora analyze plot ref_region for visualization purposes only? For example, I have a POD5 file with all the raw signals and a mapped BAM with only one read in it. Can remora visualize the region of interest like squigualiser does in signal-to-reference mode?
Thanks a lot.
The remora analyze plot ref_region command is indeed only for visualization. What is the alternative output you would like to see from this command?
I don't think the visualization output is the exact same the squigglizer output. The visualization is shown in the README in this section. The notebooks included in this repository give some examples of using the Remora API for signal visualization (either basecall, reference or "aligned" anchored). The API also can apply signal to sequence alignment refinement against either the basecalls or mapped reference sequence. If you have specific questions about these functionalities I'd be happy to answer them or point to the relevant section of the notebooks. Given that there are many ways in which users may want to visualize nanopore signal. The Remora API aims to make these tasks as easy as possible. If there is missing functionality please post here.
Closing due to inactivity.