I'm doing an RNA-seq on wheat to get differential expression of wild type vs a mutant. I'm only looking at a few specific genes. The wheat genome has not been fully sequenced, and for this problem it does not need to be. NCBI lists transcriptomes only. Can I use a program (e.g. Tuxedo suite) that requires a reference (in this case, the transcriptome) to do the differential expression? I would prefer the reference genome approach because it is simpler than deNovo assembly.