Hi all, 

 have a general question, one that I would really like some help with if somebody would be able to offer some advice. I am using R to analyse my RNA-seq data, however, I work only from the step where the sequences have been aligned and counts generated to form a counts table with ens IDs, so I am not really clued in about the alignment process. 

One thing I would like to do (is the above) but also to validate our RNA-sequencing data, to generate counts of our GFP reporter (specifically ZsG). We sort a low number of cells to carry out our RNA-seq (100s) and the population on a whole is very very rare so it is very difficult to validate by eye that our sorted cells are indeed ZsG positive. Although FACS sorting is sensitive and our gating is stringent, this would be nice to validate in our sequencing.... 

Given that this gene wont align to the mouse genome, is there a way to generate counts of ZsG in my samples? I have the raw sequencing files. 

Any help or pipeline would be greatly appreciated! 

Many thanks!