Working with some GTEx portal data right now and I've noticed that at GTEx's downloads page there are both a "Gene TPMs" and a "Transcript TPMs" file. My question is how exactly do these files differ from each other in terms of the steps for obtaining such files? I guess another way to phrase it would be why are there two files like this if RNA-Seq is supposed to output reads for transcripts in general? I would expect only 1 file with all the transcripts from GTEx instead of one that makes a distinction of gene vs. transcript... I'm obviously missing out on something rather elemental here but I don't know what it is.
Another minor question is whether or not if it is safe to assume that data from these files is normalized. As I understand, the data being TPMs implies the read counts have been normalized in the process of converting to the TPMs themselves, but I'm not 100% sure about this Thanks for any help.