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@gringene @nanopore Yes, absolutely. I am using Mus_musculus.GRCm39.dna.primary_assembly.fa as a reference, from https://ftp.ensembl.org/pub/release-108/fasta/mus_musculus/dna/
Note that this is not limited to the region I showed in that post, you can essentially pick any gene and see a similar picture.
As an example, here is a zoom of one of the alignments I get... there is obviously something odd going on...
@wdecoster @gringene @nanopore That was my first thought as well, but I see the same when importing the reference I used in IGV. Also, I used the same reference to align directly on the MinION and that one looks fine... Good suggestion, though, I will double-check again tomorrow just in case I have selected the wrong file somewhere.
@nicolaromano @gringene @nanopore you typically see things like that when the reference in IGV does not match with the reference used for alignment - i.e. the coordinates don't match with the sequence