Quantifying transcripts (as opposed to genes) with a high degree of certainty is known to be a difficult, perhaps impossible problem, especially where transcripts share a large fraction of their sequence in common. Thus all transcript quantification approaches have a certain amount of randomness and uncertainty.

This uncertainty can be quantified by using inferential replicates, or bootstraps, which can be activated in salmon using the --numBootstraps switch. Unfortunately, while tximport can ingest this data, at the moment DESeq2 can't account for these when calculating a p-value for differential expression. The swish tool (part of fishpond) can, but last time I looked it was somewhat difficult to use swish with non-model organisms.