Hi all. So I have this long read sequencing data which was basecalled and mapped using dorado and the alignment was run on default settings ( No splice awareness { Hence no N tag in CIGAR strings } ).
Now I have a BAM file, from that I want to separate my region of interest which will be anything that occupies 1 exon AND any amount of introns( they span exons and introns). After separation I want to make a GTF out of it. So that it serves as a reference whenever me( my lab ) wants to check that something maps to region of interest.
Suggest ways to do this please. I just have the BAM right now, since Dorado used minimal2 internally without being splice aware, My CIGAR strings have no N.
What I have tried so far - Using StringTie, Isoquant, both guided and unguided. But I guess they both need the G tags
EDIT: title should have been complete De-Novo GTF