Figure 4.

Splice junction detection using human real RNA-seq: comparison and agreement. The figure shows the detection of splice junctions by CRAC, MapSplice, TopHat, and GSNAP for a human six-tissue RNA-seq library of 75M 100 nt reads (ERR030856). (a) Number and percentage of known, new, and other splice junctions detected by each tool with +/−3 nt tolerance for ERR030856. (b) Venn diagram showing the agreement among the tools on known RefSeq splice junctions (KJs). Additional file 4 has pending data for novel junctions (NJs) and RefSeq transcripts. (c) A read spanning four exons (2 to 5) and three splice junctions of the human TIMM50 gene displayed by the UCSC genome browser. The included exons, numbers 3 and 4, measure 32 and 22 nt, respectively. So exon 3 has exactly the k-mer size used in this experiment. KJ: known splice junction; SJ: splice junction

Philippe et al. Genome Biology 2013 14:R30   doi:10.1186/gb-2013-14-3-r30
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