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Table 4 Comparison of SpliceJumper, TopHat2 and MapSplice2 on real data.

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

Slack value

SpliceJumper with MapSplice2

SpliceJumper with TopHat2

TopHat2 with MapSplice2

0

7,346

4,534

4,601

1

7,491

5,128

4,987

2

7,769

6,254

5,589

3

8,201

6,675

6,701

4

8,204

7,302

7,465

5

8,204

7,701

7,509

6

8,205

7,726

7,526

7

8,205

7,729

7,526

8

8,205

7,729

7,526

9

8,205

7,729

7,526

10

8,205

7,729

7,526

  1. Slack value is introduced when comparing two junctions. If the difference between both the left sides and the right sides of two splicing junctions is smaller or equal to the slack value, then we consider these two splicing junctions overlap with each other. When the slack value reaches 7, all the three tools give stable results.
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BMC Bioinformatics

ISSN: 1471-2105

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