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Table 5 The effect of quality score modeling on quantification accuracy

From: RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

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
  1. 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.