Table 5.

The effect of quality score modeling on quantification accuracy

Simulation model	Estimation model	MPE	10% EF	FP
theoretical	quality	3.1/4.1/7.2	13.8/25.2/43.5	1.0/1.8/11.6
theoretical	profile	3.1/4.1/7.2	13.9/25.3/43.6	1.0/1.8/11.7
empirical	quality	3.1/4.0/7.0	14.2/25.3/43.0	1.2/2.0/11.4
empirical	profile	3.1/4.1/7.0	14.3/25.4/43.2	1.1/2.0/11.2

Accuracy of abundance estimates from RNA-Seq data sets with different combinations of sequencing error models for simulation and estimation. Values are given as gene/global isoform/within-gene isoform.