Table 1

Accuracy measures for quantification methods applied to simulated data

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


Accuracy of five RNA-Seq quantification methods on simulated SE and PE data. Values are given as gene/global isoform/within-gene isoform.

Li and Dewey BMC Bioinformatics 2011 12:323   doi:10.1186/1471-2105-12-323

Open Data