Request methods to plot signals in a specific regions

[liuyang2006]

Dear ONT,

For POD5 files, I want to plot the raw signals with basecalled results in a region, e.g., 12-20 base-pairs. Is there a package or functions to extract the signal with related basecalling results together?

Thank you!

Best,
Yang

[Psy-Fer]

Hey,

I'm not from ONT but this might be the tool you are looking for

https://github.com/hiruna72/squigualiser

Cheers,
James

[liuyang2006]

Hi James,

This is indeed a beautiful tool! Thank you for sharing!

Best,
Yang

[marcus1487]

A bit late here, but you might have a look at Remora for raw signal plotting. Remora aims to simplify the processing steps and inputs. During basecalling you'll have to record the link between the basecalls and the signal with the --emit-moves option. After this the resulting BAM file and POD5 file (or directory of POD5s) are the only inputs to basecall anchored raw signal plotting. Adding a k-mer levels table and mapping the reads can allow comparison of the signal from many reads at a genomic location. Here are some notebooks describing the functionality. https://github.com/nanoporetech/remora/tree/master/notebooks