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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.