Figure 3: Comparison of cDNA-smMIPs with low-coverage RNA-Seq.
From: Quantification of differential gene expression by multiplexed targeted resequencing of cDNA
(a) Differences in molecule count (cDNA-smMIPs) and fragment count/read pairs (RNA-Seq) for the 12 genes targeted in the cDNA-smMIPs assay. The data points are averages over the randomly sampled sets of fragments. (b) Fraction of detected genes (genes with at least one mapped read) as a function of total number of reads. Each data point corresponds to a replicate. (c) Reproducibility of fold changes was estimated as a function of the total number of sequencing read pairs. For cDNA-smMIPs, the correlation is between log2(fold change) estimated in experiment 1 (using two technical replicates per individual) and experiment 2 (two technical replicates per individual). For the low-coverage RNA-Seq, correlation is between log2(fold change) estimated in experiment 1 (one technical replicate for respectively individual HG00117 and NA06986) and experiment 2 (one technical replicate for each individual). Each data point corresponds to a random sampling (without replacement) of the number of fragments (=read pairs) given on the horizontal axis and is based on 8 and 4 technical replicates for respectively cDNA-smMIPs and RNA-Seq. Corresponding scatter plots between the replicate DE estimates are shown in Supplementary Fig. 10. (d) Comparison of molecule counts (cDNA-smMIPs) and fragments/read pairs (RNA-Seq) mapping to the regions targeted by the cDNA-smMIPs. For each gene the average count across all smMIPs targeting the same gene is reported.
