Don’t bother with transcript level analysis

High-throughput sequencing of cDNA (RNA-seq) is used extensively to characterize the transcriptome of cells. Many transcriptomic studies aim at comparing either abundance levels or the transcriptome composition between given conditions, and as a first step, the sequencing reads must be used as the basis for abundance quantification of transcriptomic features of interest, such as genes or transcripts. Several different quantification approaches have been proposed, ranging from simple counting of reads that overlap given genomic regions to more complex estimation of underlying transcript abundances.

Here, researchers from University of Zurich show that gene-level abundance estimates and statistical inference offer advantages over transcript-level analyses, in terms of performance and interpretability. They also illustrate that while the presence of differential isoform usage can lead to inflated false discovery rates in differential expression analyses on simple count matrices and transcript-level abundance estimates improve the performance in simulated data, the difference is relatively minor in several real data sets. Finally, they provide an R package (tximport) to help users integrate transcript-level abundance estimates from common quantification pipelines into count-based statistical inference engines.


A: DTE detection performance on transcript- and gene-level, using edgeR applied to transcript-level estimated counts from Salmon. The statistical analysis was performed on transcript level and aggregated for each gene using the perGeneQValue function from the DEXSeq R package; aggregated results show higher detection power. The curves trace out the observed FDR and TPR for each significance cutoff value. The three circles mark the performance at adjusted p-value cutoffs of 0.01, 0.05 and 0.1. B: Schematic illustration of different ways in which differential transcript expression (DTE) can arise, in terms of absence or presence of differential gene expression (DGE) and differential transcript usage (DTU).

Availability – the tximport R package is available from

Soneson C, Love MI, Robinson MD. (2016) Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000 Res 4:1521. [abstract]

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