Hi All, I am currently using StringTie to identify novel transcripts (MSTRG ID transcripts) from RNAseq data in mouse. I have the gene.abund.tab output files from StringTie which gives the following info: Gene ID, Gene Name, Reference, Strand, Start, End, Coverage, FPKM, TPM. So from this file, I have the genomic loci where the assembled transcript maps to, but I don't know where to find the actual transcript sequence.
Also, an additional thing that is confusing me is that when I search the genomic location in the mouse genome using IGV, I'm finding that MSTRG transcripts are mapping to the full length known genes. How do I tell what is novel about them compared to the known annotated transcript? I'm guessing that if I know the actual sequence I can find this out.