I have a set of RNAseq data for 24 samples, half of them human culture, half of them human mixed with mouse. (Also, three replicates each with 4 treatments) For the mixed ones, about 50% of the counts map to mouse genes. I don't believe the submitters care about what's going on in the mouse genes.
Should I put mouse and human counts into DESeq2? Or just human counts?