Figure 2.

The number of read alignments from TopHat2, GSNAP, RUM, MapSplice, and STAR. Tthe RNA-seq reads are from Chen et al. [11]. TopHat2 was run with and without realignment (realignment edit distance of 0). TopHat2, GSNAP, and STAR were run in both de novo and gene-mapping modes, while MapSplice was run only in de novo mode and RUM was run only in gene-mapping mode. The number of alignments at each edit distance is cumulative; for instance, the number of alignments at an edit distance of 2 includes all the alignments with edit distance of 0, 1, or 2.

Kim et al. Genome Biology 2013 14:R36   doi:10.1186/gb-2013-14-4-r36
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