Comparison of expression estimation accuracy at transcript level.

For the HBC dataset, the R2 correlation coefficients of the logarithmic average expression measurements with the logarithmic qRT-PCR results for the eight validated transcripts under the two conditions are calculated. For the simulated dataset, the R2 correlation coefficients with the ground truth are calculated. Both single-end and paired-end simulated data are simulated. The best result for each comparison is highlighted in bold.Comparison of expression estimation accuracy at transcript level.