Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
We recently had an issue where running megalodon_extras modified_bases split_by_motif we were getting no data in the files produced. Eventually we realized this was due to our refrence genome being all lower case, and when running to isolate CG nucleotides this caused none to be found (since they were "cg" I suppose). Anyway, we changed our ref to make everything capitalized and it fixed the issue. Anyways, just wanted to point this out in case anyone else had the issue in the future. Not sure if it is "bug" exactly, but is probably worth noting in the documentation.
We recently had an issue where running megalodon_extras modified_bases split_by_motif we were getting no data in the files produced. Eventually we realized this was due to our refrence genome being all lower case, and when running to isolate CG nucleotides this caused none to be found (since they were "cg" I suppose). Anyway, we changed our ref to make everything capitalized and it fixed the issue. Anyways, just wanted to point this out in case anyone else had the issue in the future. Not sure if it is "bug" exactly, but is probably worth noting in the documentation.