Hi there. I was hoping someone can help me. I’m new to RNA-seq. I have my own RNA-seq data aligned to the reference genome as a bam file. Since this genome is poorly annotated, I would like to know if there is a way to automatically detect regions that are not present in the gtf annotation file but that have high coverage of reads in the bam file. I imagine this would allow to detect potentially unannotated genes. Then I would like to somehow mark these regions and save them in another file to inspect and perform BLAST. The genome does not have introns, so it should be straightforward but unfortunately I am not sure where to start. I hope I have explained myself well. Thank you in advance.
I think people usually do this through de novo assembly of the RNASeq. You assemble the reads into transcripts, then see if what you have matches annotated transcripts.