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Table 1 Accuracy measures for quantification methods applied to simulated data

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

  SE PE
Method MPE SE 10% EF FP MPE PE 10% EF FP
RSEM 3.1/4.1/7.1 14.1/25.1/44.1 0.9/1.7/12.0 3.1/4.0/5.2 14.4/23.3/35.7 1.0/1.8/11.3
IsoEM 4.6/5.6/8.0 18.1/29.0/45.4 1.7/3.2/31.3 4.0/4.8/5.1 16.9/25.5/35.3 1.2/1.7/11.1
Cufflinks 9.5/10.7/18.1 46.6/53.3/65.3 2.5/11.1/98.5 20.2/20.4/10.5 89.3/86.4/51.1 2.7/8.6/98.4
rQuant 8.9/12.6/43.9 44.4/58.9/89.0 7.0/16.9/99.1    
RSEM v0.6 10.1/11.2/10.4 50.5/56.0/50.7 1.4/2.9/39.5    
  1. Accuracy of five RNA-Seq quantification methods on simulated SE and PE data. Values are given as gene/global isoform/within-gene isoform.