I've asked a similar question to this before but I don't think I was descriptive enough. I had RNA-Seq done for me on a species that isn't studied very often. There is a reference genome so I have that to work with. The issue is that all the genes are predicted. I have had issues in the past where the predicted exons were completely off, so I have lost some respect for the predictions.
I was wondering if there was some kind of software that I could play with that might be able to pull out any novel transcripts and maybe even some novel isoforms. There are definitely a lot of programs that will map novel isoforms, but from what I have read, a lot of them require you to use the species transcriptome as a reference. Since I don't really trust this species transcriptome, I was wondering if there were any alternate methods? I have read paper about cufflinks but that seems rather out data?
Any help would be great!