I have a very basic question. We map the m-RNA sequence cDNA with the reference genome and then based on the alignment of the reads figure out of which of the genes were expressed. But when reference genome was created I understand that it is iterated continuously to map the best possible genome.
But no genome can be perfect that can be referred. So if we are mapping a cdna and saying that the gene is deferentially expressed, it is quite possible that the reference genome has a snp and the read under consideration is correct.
I am confused with this whole reference genome mapping. Can someone help me get a more clear picture