I'm setting up my first RNAseq experiment and I'm wondering what the opinion is of those with more experience. I have 50 samples, 25 from the control group and 25 from the treatment group. I'm really only interested in determining if a handful of immune genes are upregulated in my treatment group. Is 12 the max # of samples that can be multiplexed in a single lane? If so, how do I determine what my coverage would be for each sample? How do I determine what the coverage is for a different number of samples (X) on a lane? Right now, I'm thinking that I can put 6 samples on a lane, which would get me 16+ mil reads per sample, then just run 8 lanes. Is that correct? Is 16M reads sufficient for this type of question?