Download all eQTL data for all the 9 tissues from GTEx Portal

Question

[komal.rathi]

Hi,

We are working on eQTL analyis of Human Heart samples and would like to use the eQTL data (for all the 9 tissues like Adipose Subcutaneous, Artery Tibial, Blood, Heart Left Ventricle, Lung, Muscle Skeletal, Nerve Tibial, Skin Sun Exposed, Thyroid) from GTEx for the sake of comparison. However, I find that I can only download/copy data for 1000 most significant SNPs for any gene per tissue (Go to http://www.gtexportal.org/home/ -> Search -> Search eQTLs -> Browse Significant eQTLs -> Select Tissue). You have to click on the + sign on the left side of a Gene-SNP (most significant) pair entry to expand it and find all other SNPs related to that gene. But I would like to download all the eQTL data i.e. all SNPs per gene in each of the 9 tissues. Has anyone been able to do that? Any help would be much appreciated.

Thanks to @rbagnall, the data is available here: https://www.gtexportal.org/home/datasets

[sekharsj]

Hi Komal,

Did you manage to download that data, now? Even I wanted it and couldn't figure out the way to get it.

[komal.rathi]

sekharsj No, I couldn't. Like I said, you can download data only for 1000 most significant SNPs for any gene per tissue. They haven't released the complete data just yet.

[sekharsj]

Thank you Komal. I am sure that you are working on Genomics too. can you drop an email on [e-mail]?

Answer 1

[Ana]

One of the investigators involved in the GTEx (Tuuli Lappalainen) replayed on twitter: "I think that GTEx eQTL bulk downloads aren't available before pilot paper publication. Will confirm.".

Often these consortia give prepublication access to all their data upon request. I suggest you email them about it.

[komal.rathi]

Thanks Ana

I did email them and they said the full eQTL data should be released in a few weeks.

Answer 2

[AlexAbdulkaderKheirallah]

Is all the data from GETx available now?. In addition to significant associations I'm also interested in the P-values for non-significant associations. Are these available now?

Answer 3

[kunal368]

I am looking to download the same data. Is it possible to download now? Nobody has been able to download?

[rbagnall]

Yes, from here: https://www.gtexportal.org/home/datasets

Scroll down to single tissue eQTL data or multi tissue eQTL data. Read the descriptions, some files are very large.

[komal.rathi]

Can you move this to an answer so I can accept it? Thanks!