Table 4

Recall of splice junctions identified from EST data

Species

SpliceGrapher

Supersplat

TopHat

A. thaliana

24,757

25,590

22,934

V. vinifera

35,403

37,291

34,081

We compared the splice junctions that each package identified in RNA-Seq data to splice junctions inferred from ESTs aligned to A. thaliana and V. vinifera. Numbers represent the number of splice junctions from spliced alignments of RNA-Seq data that were also identified from alignments of ESTs (excluding junctions that are annotated in TAIR9). Despite performing a step of filtering of false positives, SpliceGrapher achieves a higher level of recall than TopHat, and only slightly lower than SuperSplat.

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