I have a large Illumina RNA-Seq dataset, and I have already mapped it to the reference genome using STAR and done quantification. But now I want to look at expression of GFP which is not native to the species (as this is a transgenic mouse).
I imagine the 'proper' way to do this is to create a new reference genome with the GFP gene added as an extra chromosome. But this would then require a lot of duplicated work, space, and time.
What I tried to do is create a new reference index with the single GFP gene, and then align against that, but STAR creates a 1.5GB index for this single gene, and what if I want to do this with more genes? This seems to using STAR outside the type of work it was originally designed for. Or is this in fact the correct approach?
Am I missing anything obvious here, like using BLAST or BLAT (I don't have any experience with these older tools)? Thanks.