. 2016 Feb 29;4:1521. Originally published 2015 Dec 30. [Version 2] doi: 10.12688/f1000research.7563.2

Table 2. Summary of suitable analysis approaches for the three types of comparative analyses discussed in the manuscript (DGE, DTE and DTU).

Task	Input data	Software (examples)	Post-processing
DGE	Aggregated transcript counts + average transcript length offsets, or simple counts + average transcript length offsets	Salmon, kallisto, BitSeq, RSEM
		tximport
		DESeq2, edgeR, voom/limma
DTE	Transcript counts	Salmon, kallisto, BitSeq, RSEM	Optional gene-level aggregation
		tximport
		DESeq2, edgeR, sleuth, voom/limma
DTU/DEU	Transcript counts or bin counts, depending on interpretation potential ¹⁸	Salmon, kallisto, BitSeq, RSEM	Optional gene-level aggregation
DTU/DEU		DEXSeq	Optional gene-level aggregation