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Table 1 Comparison of SpliceJumper, TopHat2 and MapSplice2 on simulation data.

From: SpliceJumper: a classification-based approach for calling splicing junctions from RNA-seq data

Slack value

Test1 dataset

 

Test2 dataset

 
 

SpliceJumper

TopHat2

MapSplice2

SpliceJumper

TopHat2

MapSplice2

0

0.8314

0.0003

0.8918

0.7940

0.0015

0.8288

1

0.8923

0.0016

0.9627

0.8548

0.0103

0.9319

2

0.9367

0.9370

0.9631

0.9156

0.8558

0.9328

3

0.9618

0.9377

0.9639

0.9400

0.9016

0.9471

4

0.9666

0.9384

0.9642

0.9491

0.9150

0.9473

5

0.9676

0.9390

0.9647

0.9495

0.9156

0.9476

6

0.9676

0.9396

0.9650

0.9562

0.9166

0.9485

7

0.9676

0.9397

0.9650

0.9573

0.9167

0.9502

8

0.9676

0.9397

0.9651

0.9578

0.9178

0.9508

9

0.9677

0.9397

0.9651

0.9578

0.9178

0.9508

10

0.9677

0.9398

0.9651

0.9578

0.9178

0.9508

11

0.9677

0.9398

0.9651

0.9578

0.9179

0.9510

12

0.9678

0.9399

0.9651

0.9578

0.9179

0.9510

13

0.9678

0.9399

0.9652

0.9579

0.9180

0.9510

14

0.9678

0.9399

0.9652

0.9579

0.9180

0.9510

15

0.9678

0.9400

0.9653

0.9579

0.9180

0.9510

  1. Slack value is introduced when comparing a called out junction with a benchmarked one. And if the distance of both sides between the called out one and the benchmarked one is within the slack value then the called out one is considered as a correct one. We compare the F-value (2*Precision*Recall/(Precision+Recall)) of the three tools for different slack values. The higher the F-value the better the performance.
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BMC Bioinformatics

ISSN: 1471-2105

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