I used the Annotate DESeq2/DEXSeq output to generate gene IDs. Here, the gene ID is associated with the genome (see pic) in column 1. For example it looks like MSTRG.10188| App. Nothing appears in column 13 where the gene name (in this case App) should be. Can you please help!
check information available in the annotation file for any gene in question, such as MSTRG.10188. Are there information available or not? It looks like StringTie gene name, so there might be very little/no info.
Many organisms have annotated genes. Consider using a public annotation. Even these might have predicted/unknown genes.