Sequencing depth was more influential than read length in ensuring consistent DEG results
Two of the main technical parameters that determine cost in an RNA-Seq experiment are (i) read length and (ii) sequencing depth. The impact of read length on the ability to accurately measure DEGs has not been comprehensively studied to date: One previous study utilized data from the SEQC study and determined virtually no impact of using paired-end reads vs. single-end reads on the ability to reproducibly detect top 200 DEGs when sorted by p-value and log2 fold change (Impact of read length and sequencing depth on DEG detection. Impact of read length and sequencing depth on Jaccard index between DEGs (Site 1). The Jaccard index represents the proportion of intersecting DEGs compared to the union of DEGs identified for a subsampled/truncated dataset and the original dataset.