**4. Discussions**

**3.6. The effect of gene models on differential analysis**

440 Next Generation Sequencing - Advances, Applications and Challenges

sent Log2(count + 1).

Generally, RNA-seq differential analysis requires biological replicates. However, we analyzed 16 different single tissue samples. To demonstrate the effect of gene models on differential analysis, the fold changes between heart and liver samples were calculated using RefGene and Ensembl annotations. The correlation of the calculated Log2Ratio (liver/heart) was depicted in Figure 10. The graph should show a perfect diagonal line if the choice of a gene model has no effect on differential analysis. Although the majority of genes have highly consistent or

**Figure 8.** The correlation of gene quantification results between RefGene and Ensembl. Note both x and y-axes repre‐
