Recent breakthroughs in bioinformatics tools for quantification (e.g. Cufflinks/Kallisto/Salmon etc.) and tools which can identify differential transcript usage (DTU) (e.g. DRIMSeq, Cufflinks etc.) mean that from RNA-seq data we can now relatively easy obtain a genome wide analysis of transcripts that are differentially used betwen conditions.
What can you use these results for? What systematic analysis does this transcript level data enable?