Differential Expression Analysis Comparison

We used DESeq2 to find differentially expressed transcripts in control diet and iron-loaded diet samples for each sequencing depth. The FDR was adjusted to 0.05, and the other parameters were set to default. The number of overlapping differentially expressed transcripts in Trad-KAPA and 3’-LEXO was calculated. For 1, 2.5 and 5 million reads, the overlap between differentially expressed transcripts in subsampled pools and the initial 10 million read sample was computed. The log fold changes from DESeq2 were used to calculate the correlations between the two methods.