I have some RNA-seq data for a large number of samples (treated vs control), to the order of ~50M PE reads per sample, from mouse. These data have not been aligned yet to the reference genome.
I am, however interested in the expression level of one single target gene across all these samples, and a quantification of whether it is differentially expressed between treated and control.
Is there a quick way of doing this, where I can bypass alignment to the whole genome, but only align to the target gene of interest? (An alignment-free method like kallisto/sleuth may be another option, it just occurred to me, but I was wondering more about a brute-force alignment to target method)