text: user7354: 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.
  
  user4766: 
  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.
  
  
original_text: 7354: <p>I would like to download RNAseq gene expression data from GTEx from the liver only. What is the best way to do this?</p>
  
  <p>I have tried a few things. I downloaded several files from the GTEx website (<a href="https://www.gtexportal.org/home/datasets" rel="nofollow noreferrer">https://www.gtexportal.org/home/datasets</a>, under "RNA-Seq Data"), but the problems I run into are:</p>
  
  <ul>
  <li>Not sure what is the best file: "Gene read counts" or "Gene TPMs"? What is the difference?</li>
  <li>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?</li>
  <li>How can I download the data for liver tissue only, instead of ALL data for ALL tissues?</li>
  </ul>
  
  <p>Thank you for suggestions.</p>
   4766: <ul>
  <li>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.</li>
  <li>I have not noticed that there are duplicated genes in those files, can you show an example?</li>
  <li>I do not think you can download expression from one tissue, but you can always subset. The whole dataset is not very large.</li>
  </ul>
  