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

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.

ISSN: 1474-760X