Normalized FPKM calculation and box-plot generation for tU-labeled nascent RNA

In order to normalize the RNA-seq FPKM values of the untreated and peroxide treated cells, the reads of the S. pombe spike-in were set to be equal, and the FPKM values were adjusted accordingly. Normalized FPKM values of all SAGA and TFIID dominated genes were used to generate the boxplot in Figure 2, displaying the 95^th, 75^th, 50^th, 25^th and 5^th percentile.