Comparison of expression estimation accuracy at gene level using various datasets.

For the MAQC and HCC datasets, the R2 correlation coefficients of the logarithmic average expression for the matching PCR-validated genes with the logarithmic qRT-PCR or qPCR results are calculated. Two samples (HBR and UHR) in single-end (SE) data (SRA010153) and one sample (UHR) in paired-end (PE) data (SRA012427) are used for the MAQC dataset. Seven lanes with 9 million paired-end reads for each lane are used for the HCC dataset. For the simulated dataset, the R2 correlation coefficients of the estimated gene expression with the ground truth are calculated. Both single-end and paired-end simulated data are used. The best result for each comparison is highlighted in bold.Comparison of expression estimation accuracy at gene level using various datasets.