Normalization method

[yuxinPenny]

Dear authors,

I was using the remora API to see the signal refinement results. After generating the IO_Read object from BAM and Pod5 file, I can query the normalized signal. I am wandering how the signal is normalized.

[marcus1487]

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 to apply the "rough rescale" method. This ensures that the quantiles of the expected levels (from the k-mer table) match the quantiles of the observed levels (from the signal). Thus the alignment of the io.Read sequence do not need to be well aligned to the bases as is performed by the signal mapping refinement for signal plotting. The implementation of this process can be found here.