I was going through the workflow "Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification" which can be found here, https://f1000research.com/articles/7-952/v3#f4 and I wanted to clarify something.
Under the section DTE evaluation there is a sentence that says "For this assessment, all of the simulated non-null transcripts count as true positives of differential transcript expression, whether they originate from the simulated “DGE”, “DTE”, or “DTU” genes. For most of the methods, we simply provided the transcript-level data to the same functions as for the DGE analysis."
As mentioned there are investigators that prefer to assess DE on a per-transcript basis, does this mean one could use DGE methods at the transcript level?Is DTE in essence capturing any transcript that is DE, regardless of that status of that transcript (i.e. how many transcripts are expressed, and if the total gene-level does not change)?