Skip to main content

Table 1 RNASEG results on simulated data

From: Transcript mapping based on dRNA-seq data

  

a

F-measure

Recovered sequencing data [%]

 

u

 

1

10

100

1,000

1

10

100

1,000

t = 1 (170 h)

 

1

0.93

0.93

0.93

0.93

100.00

100.00

99.95

97.92

 

10

-

0.93

0.92

0.93

-

100.00

99.96

98.10

 

100

-

-

0.86

0.86

-

-

99.91

99.12

 

1,000

-

-

-

0.67

-

-

-

97.73

t = 100 (156 h)

 

1

0.93

0.93

0.93

0.92

100.00

100.00

99.96

98.63

 

10

-

0.93

0.92

0.92

-

100.00

99.96

98.10

 

100

-

-

0.86

0.86

-

-

99.91

99.12

 

1,000

-

-

-

0.67

-

-

 

97.73

t = 1,000 (110 h)

 

1

0.87

0.86

0.83

0.81

100.00

99.98

99.83

97.76

 

10

-

0.86

0.83

0.81

-

99.98

99.83

97.76

 

100

-

-

0.82

0.80

-

-

99.81

97.76

 

1,000

-

-

-

0.67

-

-

-

97.75

  1. F-measure and fraction of recovered sequencing data from the secondary library (in %) for simulated data. RNASEG was applied to the forward strand of region 684,676 to 987,046 of the H. pylori genome. We set k ̂ = 20,000, cp ̂ = 1,000, w = 100, and varying values for parameters t, a and u. We define: True positives (TP) are genes that are part of a transcript segment, true negatives (TN) are intergenic regions that are not part of a transcript segment, false positives (FP) are intergenic regions that are part of a transcript segment and false negatives (FN) are genes that are not part of a transcript segment. ‘-’ indicates parameter combinations that have not been tested because they are not sensible. Numbers in brackets below t correspond to the average runtime in CPU hours for all simulations with this value of t.
Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us