Traditionally, RNA-seq data was quantified on gene level. Newer methods quantify on transcript/isoform level. For example, Kallisto only outputs transcript-level abundances. From the DESeq2 vignette:
A newer and recommended pipeline is to use fast transcript abundance quantifiers upstream of DESeq2, and then to create gene-level count matrices for use with DESeq2 by importing the quantification data using the tximport package.
Is it just for consistency and/or simplicity that the values are converted to gene level? Would it better to proceed with transcript-level table or does that violate some DESeq2 (or similar tools) assumptions?