The number of read and spliced-read alignments from TopHat2, using different realignment edit distances and no realignment. Edit distances of 0, 1, and 2 were used. As TopHat2 allows more realignment from no realignment to 2 to 1 to 0, the number of read alignments and spliced-read alignments increases, so that the differences in the numbers of read alignments from TopHat run with different realignment edit distance are mostly explained by the increase in the number of spliced-read alignments.
Kim et al. Genome Biology 2013 14:R36 doi:10.1186/gb-2013-14-4-r36