RNAseq gene expression estimates altered by trimming parameters and choice of genome alignment

One potential confounder of RNAseq analysis can result when applying a standardized pipeline to samples of different sexes in species with chromosomal sex determination. Because of the homology between the human X and Y chromosome, we expect that mis-mapping will routinely occur between these two chromosomes, artificially affecting estimates of sex-linked gene transcription. For this reason we tested alternative alignment scenarios on RNAseq samples from the brains of 5 genetic female and 5 genetic males to assess how inferences of differential gene expression patterns change depending on the reference genome.