I have a set of mouse samples genetically engineered to express a single human gene. I have performed alignment against the mouse genome with STAR, and am trying to find a way to recover those reads that were mapped to this single human gene.
My current thinking is to identify the unmapped reads from each sample and then realign them against the human reference genome, subsetted to include only the chromosomal region corresponding to this human gene of interest. I will also filter the GTF annotation file to include only the entry corresponding to this gene.
Any thoughts on the approach above and alternative suggestions are welcome!