more accurate than expression arrays and with a higher dynamic range (i.e. coefficient of variation <0.1 for at least 12,000 genes; Supplementary Figure 3). RNA-Seq allows one to evaluate allele-specific expression in heterozygous individuals, improving the power to identify cis regulatory variants. With the target depth of 50 million aligned reads, we expect to be powered to detect ASE in the top tertile of expressed genes (Supplementary Figure 4). As the cost of RNA-Seq drops, greater read depth will be possible, but with current resources the strategy is to maximize the number of samples analyzed.
