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(a) Boxplots of the within-MCF-7, within-SUM-102, and between-group square root of JSD of all genes for all methods. (b) A case where Cufflinks underestimated the difference between the two groups. The second isoform of Gene AIM1 has a unique first exon, whose read coverage differs significantly between the two groups. A detailed plot with all eight samples can be found in Appendix Figure 11a.
