How to download RNAseq gene expression data from GTEx
Gene read counts are the number of reads or fragments that are mapped to each gene. So it is an integer and the values are not directly comparable between samples due to differences in sequencing depth. TPM stands transcripts per million. It is the normalized gene expression level. Basically, you first normalize read counts by gene length and then normalize the library size to 1e6 in all libraries. As for which one should you use, it depends on what analysis you want to do and what tool you are going to use.
I have not noticed that there are duplicated genes in those files, can you show an example?
I do not think you can download expression from one tissue, but you can always subset. The whole dataset is not very large.