3' RNA sequencing does not increase power or reduce costs for gene expression analysis

Sequencing RNA transcripts for gene expression profiling is a popular and important technique with broad utility in biological sciences. We set out to comprehensively compare the two most popular methods for generating sequencing libraries for differential gene expression analysis: 3′-end sequencing, which generates libraries from the 3' end of an RNA transcript; and traditional RNA sequencing, which generates libraries from whole RNA transcripts. We include three species in our experiment to test whether our findings replicate across genomes and genome assemblies. We found similar levels of precision and power to detect differentially expressed genes between the two methods. Notably, whole transcript RNA-seq performed better in the non-traditional model species included in our study. Overall, we recommended whole transcript RNA sequencing for the added benefits of alternative splicing detection, and gene-body variant detection. ### Competing Interest Statement The authors have declared no competing interest.