I have been trying to find the difference between the above two online for a while now, but I haven't got a satisfactory answer. I also didn't find a similar question on Biostars, so I thought of formally asking it now.
Tximport (and maybe other tools too) gives a couple of outputs for each gene, and two of them are - abundance and counts. What is the difference between them?
This paper gives a general idea that count based methods assign reads to genes directly, whereas abundance based methods assign abundance of each transcript with a probabilistic model that makes use of info such as fragment length distribution etc.
So, having said that, is this really the difference between the abundance and count values that I get for any gene from Tximport (or any tool in general)? And, in which situation is one of them a more meaningful/desirable quantity?