Comparison of RPKM Gene Expression Scores Reported by SAMMate, Novoalign and Tophat. (a) Comparison of the overall RPKM distributions calculated by different methods. 'S' stands for SAMMate, 'N' stands for Novoalign, and 'T' stands for Tophat. '1' and '2' represent two biological replicates of the wild type transcriptome (control). '7' and '8' represent two biological replicates of the miRNA-155 transfected transciptome (treatment). For example, 'S1' stands for the RPKM score distribution calculated from the first biological replicate transcriptome of wild type Mutu I cell line using SAMMate. There are no significant differences both visually and statistically. (b) Piechart of percentages of gene fold changes calculated by each tool that are closest to the 3'-UTR experimental results. SAMMate is superior to the other competing tools.