Table 3

Comparison of splice junctions identified by each package

SpliceGrapher

Supersplat

TopHat

A. thaliana

Canonical junctions (GT-AG/GC-AG) within genes

80,421

84,744

83,367

Junctions in common

-

74,821

63,710

Novel junctions

4,969

7,255

14,572

Novel junctions with a false-positive site

-

3,077

9,942

Novel junctions in common

-

3,599

1,982

V. vinifera

Canonical junctions (GT-AG/GC-AG) within genes

74,457

82,281

65,439

Junctions in common

-

70,554

59,154

Novel junctions

9,831

13,394

6,307

Novel junctions with a false-positive site

-

4,040

1,899

Novel junctions in common

-

8,020

3,662

Side-by-side comparison of canonical splice junctions identified by each package, reconciling differences between SpliceGrapher and the other two packages for A. thaliana (top half) and V. vinifera (bottom half). For each species we show the number of canonical splice junctions each package found recapitulated in the RNA-Seq reads. For Supersplat and TopHat we also show the number of junctions each shares with SpliceGrapher and the number of novel junctions for which SpliceGrapher's classifiers identified either the donor site or the acceptor site as a false positive.

Rogers et al. Genome Biology 2012 13:R4   doi:10.1186/gb-2012-13-1-r4