I am currently analyzing some RNA seq data derived from mice that express the reporter, tdtomato, under an endogenous promoter. I'd like to get read counts for tdtomato, but obviously it isn't part of the mouse transcriptome, and therefore Salmon doesn't map reads to it.
From what I can figure out on my own, it seems this shouldn't be that hard. Just add the sequence for tdtomato to the mouse transcriptome that I supply to Salmon. And if I want gene level counts, add the tdtomato accession number to my tab delimited transcipt to gene mapping file. Anything else to be done or to look out for? Thanks!