I am working on a collaboration and we recently generated some RNA-seq data. So the lab that we are working with inserted a human gene into the Drosophila genome to see the effects of a specific mutation. They were able to insert the gene and did some RNA sequencing. I was given the task of working with the RNA-seq data but I have no idea how to find this gene that was inserted. I've worked with RNA-seq data in the past but never like this. How an I suppose to find the gene? I know there are programs out there to find novel isoforms found in RNA-seq data but what do you do when you're looking for an entire gene.

I thought about trying to somehow add the human gene into the Drosophila index? but the index is very specific about gene location right?

I think this is an easy question but I'm not sure where to begin here. Any help would be amazing.

Thanks!