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I am new to the field of Bioinformatics. GTEx database is great; I know how to check whether a SNP is eQtl with the online tools of GTEx.

But my question is how to download the right data to draw a boxplot on my own. like this paper: Figure 1 in this paper

Please help me . I have been stuck on this for many days.

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  • $\begingroup$ I agree that GTEx is great, however for SNP variation however, I recommend using gnomAD due to sheer number —and the high possibility that a reviewer will ask the same. $\endgroup$
    – Matteo Ferla
    Mar 29, 2020 at 7:59
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    $\begingroup$ In recent years violin plots have taken over bloxplots as the common way to show such data —assuming few dataseries. Yes, five years ago showing a violin plot always required explaining but now the broader scientific community understands them. $\endgroup$
    – Matteo Ferla
    Mar 29, 2020 at 8:03
  • $\begingroup$ @MatteoFerla THX for your note. I will go to learn how to use gnomAD. Would you please give me some hints that how to download the genotype data of a SNP (eg, sample 1 is AA ; sample 2 is AG, etc) from GTEx . I really want to know . $\endgroup$
    – gong.y
    Mar 29, 2020 at 11:11
  • $\begingroup$ @MatteoFerla I want to perform eQTL analysis from GTEx. Help me please and that will save my life! $\endgroup$
    – gong.y
    Mar 29, 2020 at 11:29
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    $\begingroup$ Cross-posted: biostars.org/p/429533 $\endgroup$
    – ATpoint
    Mar 29, 2020 at 12:00

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There are two types of data you can get from GTEx. The first is summary statistics, basically the slopes and p-values you see in the boxplot. You can also get expression levels for all genes measured in GTEx.

However, in order to plot boxplot by yourself, you also need genotype data. This is not publicly available because of privacy issues. In order to get it, you have to apply to it on dbGaP. I think you can find relevant information on the GTEx website.

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