I would like to download RNAseq gene expression data from GTEx from the liver only. What is the best way to do this?
I have tried a few things. I downloaded several files from the GTEx website (https://www.gtexportal.org/home/datasets, under "RNA-Seq Data"), but the problems I run into are:
- Not sure what is the best file: "Gene read counts" or "Gene TPMs"? What is the difference?
- I would like 1 value per sample per gene. There are many duplicate genes in these 2 files. How can I collapse them to 1 value per gene?
- How can I download the data for liver tissue only, instead of ALL data for ALL tissues?
Thank you for suggestions.