Figure 6

Sequencing depth and the detection of differentially expressed genes. A) Venn diagram showing the overlap between the total numbers of DE genes found at the different sequencing depths. B) Distributions of absolute log₂ fold changes for the DE genes found at each sequencing depth. C) The 194 genes deemed as DE exclusively at 17 M read depth (but not at higher read depth), plotted as log₂ read count vs. log₂ fold change at three distinct read depths (orange points), along with not significantly DE genes (grey points) and genes significantly DE at all read depths (pink points). As read depth increases, the estimated fold changes for genes with low mean read count decreases, suggesting that the estimation of DE at lower sequencing depths suffers from sampling errors for genes with low read count. D) More plots of log₂ read count vs. log₂ fold change for all genes at all three respective sequencing depths. Genes detected as DE exclusively at a 50 M read depth (896 genes in total) are shown as green points.