How to create modified basecalling dataset with nanopore data with an ambiguous motif sequence?

Question

[swim1128]

What can I use to create a modified basecalling dataset from nanopore data when my motif has ambiguous bases? Usually Remora is used for work like this, except some of the bases in my motif are ambiguous (GTNNaNNTGG pos 5), and Remora can't handle ambiguous bases. Thus, I am unable to prepare the chunk dataset.

[GenoMax]

What can I use to create a modified basecalling dataset from nanopore data

What do you mean by this? You call modified bases from a list dorado supports. Currently it supports m6A_DRACH, 6mA, m5C, 5mC, inosine_m6A, 5mCG_5hmCG, m6A, 5mCG, pseU, 5mC_5hmC, 4mC_5mC. Where does motif come in?