Fig. 5
Sex chromosome complement informed alignment calls more sex-linked genes as being differentially expressed. a Sex differences in the gene expression, log2(CPM + 0.25/L), between the twenty samples from genetic males and females are shown when aligning all samples to the default reference genome (left) and a reference genome informed on the sex chromosome complement (right) for the brain cortex. Each point represents a gene. Genes that are differentially expressed, adjusted p value < 0.01, are indicated in black for autosomal genes, blue for Y-linked genes, and red for X-linked genes. b We show the overlap between genes that are called as differentially expressed when all samples are aligned to the default genome, and genes that are called as differentially expressed when aligned to a sex chromosome complement informed genome. When samples were aligned to a reference genome informed on the sex chromosome complement, 27 genes were called as differentially expressed between the sexes, of which 4 were uniquely called in the sex chromosome complement informed alignment. There were no genes that were uniquely called as differentially expressed when aligned to a default reference genome