We have some RNA from knock-in mice, there are two different sequences we're looking for. We have aligned to the mouse genome using STAR but the sequence isn't there which isn't too surprising What is the best way to check for the presence of the sequence? Should I just turn them into a sequence and use them as the reference genome for STAR to align to? Is there a way I can easily incorporate it into the existing genome so I could get read counts for everyhting including those reads? Should I just BLAST using something like magicblast?