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Table 3 Comparison of splice junctions identified by each package

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

  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
  1. 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.