I have HiSeq data from mice exposed to two conditions. I would like to answer the following question: "Is there a significant difference in mRNA transcript levels when comparing condition A to condition B?"
To answer this question, do I have to map my HiSeq reads to the reference genome to determine expression values or is it acceptable to use a small set of reference sequences of interest (approx. 50)? These particular sequences are not annotated on the reference genome. What are the downsides to not mapping to the genome?