Question: Download all eQTL data for all the 9 tissues from GTEx Portal
2
gravatar for komal.rathi
5.5 years ago by
komal.rathi3.5k
Children's Hospital of Philadelphia, Philadelphia, PA
komal.rathi3.5k wrote:

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

eqtl gtex portal • 5.7k views
ADD COMMENTlink modified 6 weeks ago by genomax74k • written 5.5 years ago by komal.rathi3.5k
1
gravatar for Ana
5.5 years ago by
Ana30
London
Ana30 wrote:

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.

 

ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by Ana30

Thanks Ana 

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

ADD REPLYlink written 5.5 years ago by komal.rathi3.5k
0
gravatar for sekharsj
5.1 years ago by
sekharsj0
European Union
sekharsj0 wrote:

Hi Komal,

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

 

ADD COMMENTlink written 5.1 years ago by sekharsj0

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.

ADD REPLYlink written 5.1 years ago by komal.rathi3.5k

Thank you Komal. I am sure that you are working on Genomics too. can you drop an email on sekharsj@gmail.com ?

ADD REPLYlink written 5.1 years ago by sekharsj0
0
gravatar for FreeMindAlex
3.7 years ago by
FreeMindAlex100
United Kingdom
FreeMindAlex100 wrote:

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?

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by FreeMindAlex100
0
gravatar for kunal368
5 months ago by
kunal3680
Cincinnati Children Hospital Medical Centre
kunal3680 wrote:

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

ADD COMMENTlink written 5 months ago by kunal3680

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.

ADD REPLYlink written 5 months ago by rbagnall1.4k

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

ADD REPLYlink written 6 weeks ago by komal.rathi3.5k
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