Hi all, I'm looking for some help in quantifying the number of transcripts in a virus genome from nanopore RNAseq data. I've currently been mapping the RNAseq data back to the reference genome using minimap, and then running Nanosplicer and stringtie to quantify the number of transcripts. Nanosplicer should in theory give the number of reads mapping to a certain transcript, but due to our data falling under the SIQ value, it hasn't, and instead only gives a list of splice sites. I've been using that splice sites as a reference to feed into stringtie so that stringtie can quantify the number of read that map to each transcript, but the problem is that often the number of reads that map to a particular transcript does not seem to correspond to the number of transcripts we see in the coverage map under IGV. Is there a known pipeline splice variant calling and quantification for Nanopore RNAseq data?