SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data

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.

ISSN: 1474-760X