I´m trying to use this program "https://easygwas.tuebingen.mpg.de/" in order to perform an experiment with my own data, but when I upload the file, this message comes out: "[500] URL not found". Has anybody used the page? I´ve tried for several days but didn't have any luck.
Thank you!
Tutorial 2 has a demo file that you can try. I just used it and performed GWAS with no problems. It seems to be working fine. QQ-plots for individual chromosomes did not show though. Hope you can make it work with your own data (check the file format you are using). Cheers!
Thank you Daniel. I could run the tutorial file, but no mines... I´ll check the format again.
Another question, do yo know how to change the threshold from 6.5 to 5, for example?
I wish I could be of more help, but it's difficult without knowing further specifics about your experiment, like what kind of data you are trying to use, or which error messages you are getting.
(1) Your data is just phenotypic or genotypic also? (2) What is the species? (3) Which GWAS algorithm are you trying? Linear regression? (4) Which steps can you go through before you get an error?
The threshold you are referring to, is it the mAF? If so, I guess they only give a set for you to choose from.
On a side note, have you tried contacting the developers for some help? Maybe you can get more useful help with them by email.
Cheers!
Daniel! Thanks for your help! I could finally run my data! I´m working with Arabidopsis thaliana. I have only phenotypic data. Initially i´m trying with the linear regression. This is my first experience with the gwas so I still don´t have much idea on how to perform the gwas...
What i meant with the threshold is: when you see the manhattan plot, there is a green line set at a bit more than 6 (sorry I explain this way but i think it is easier to visualize). I was told that with this program you can change it and set it lower. Is it right?
Thank you!!!
That's great! I'm glad you got it working. The threshold shown is the statistical significance for the multiple hypothesis testing for 0.05 significance. You can change that by clicking on the GWA result options link at the top of the plots page.
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