Additional file 19 of Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data

Additional file 19: Gencode sex chromosome complement informed transcriptome reference eliminates Y-linked expression in female XX samples. A) Sex differences in gene expression, log2(CPM + 0.25/L), between the sixteen samples from genetic males and females are shown when aligning all samples to the default gencode reference transcriptome (left) and a reference transcriptome informed on the sex chromosome complement (right) for 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 overlap between genes that are called as differentially expressed when all samples are pseudo-aligned to the default transcriptome, and genes that are called as differentially expressed when pseudo-aligned to a sex chromosome complement informed transcriptome reference. When samples were aligned to a reference transcriptome informed on the sex chromosome complement, 17 genes were called as differentially expressed between the sexes. ZBED1 was uniquely called as differentially expressed when aligned to a default reference genome.