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Table 2 F-measure [in %] for spliced reads with different number of spanned junctions for simulation 1

From: ContextMap 2: fast and accurate context-based RNA-seq mapping

Program

Number of junctions spanned

 

1 (13808336)

2 (598297)

3 (11781)

2* (548382)

3* (6908)

CM Bwt1

91.47

14.24

-

15.16

-

CM Bwt2

94.03

78.47

50.21

82.37

72.66

CM Bwa

95.03

82.73

53.33

86.67

76.46

CM Bwa ann

95.74

84.65

53.9

88.47

76.79

MapSplice 2

92.42

79.18

27.27

80.65

3.44

STAR 1-pass

77.63

30.91

5.01

31.91

1.49

STAR 1-pass ann

93.55

81.65

75.71

82.57

82.17

STAR 2-pass

95.0

85.55

82.07

86.59

87.29

STAR 2-pass ann

95.07

86.28

82.55

87.02

86.49

TopHat1

87.83

77.51

63.57

80.42

75.56

TopHat1 ann

88.02

78.99

68.13

81.06

76.1

TopHat2

91.71

87.0

76.92

89.66

88.51

TopHat2 ann

94.84

90.79

85.92

92.05

90.35

GSNAP

83.13

43.45

18.52

42.35

12.29

GSNAP ann

96.47

88.59

79.51

89.86

84.67

  1. *The last two columns show results only for reads for which all exons except the first and last exon had length ≥ 20 nt. For this evaluation, read alignments were only considered a true positive if all simulated splice junctions in the read were recovered and no additional splice junctions were identified. Indels were ignored for this purpose. Recall and precision values for both simulations can be found in Additional file 1: Table S5.
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BMC Bioinformatics

ISSN: 1471-2105

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