I am thinking whether or not to apply dog transcriptome annotation in the optional transcriptome alignment of TopHat2. I don't think it would hurt unless the quality of transcriptome annotation is really bad and gives us wrong information. I am new in the RNA-seq research. From my point of view, it looks like only human and mouse transcriptomes are considered well-annotated (or maybe I am wrong).
How about your opnion on the dog transcriptome (Canis familiaris)? Would it hurt to apply it in the TopHat2?