Gene-mapping option is SNP2GENE

[ANDREW MORRIS]

Hi Team. I have been running the latest version of FUMA. In the SNP2GENE function, we used to have to select one of position mapping, eQTL mapping, or chromatin interaction mapping. In the new version, there is the additional option of xQTL mapping - which is great! However, when I try to select eQTLs from the xQTL mapping list, I get the warning that I need to select one option from positional, eQTL and chromatin interaction mapping. It is only when I also select the deprecated eQTL mapping that I am able to submit the job - and the gene mapping is then only based on the dataset selected from the eQTL analysis (and not xQTL). Could you help please! Many thanks in advance!! Andrew

[Tanya Phung]

Hi Andrew, 

Thank you for reporting the issue. 
I had applied a fix. It should let you submit a job with selecting just the xQTLs mapping. 

I also wanted to point out/clarify that in the Results section, the Mapped Genes tab would contain results from positional, (legacy) eQTLs, and ciMap if any of these options were selected. 
For the xQTLs mapping, these results are found in the xQTLs tab. 

Best,
Tanya

[ANDREW MORRIS]

Thanks Tanya for the quick response. I'm now able to get SNP2GENE to work using just the xQTL option - using GTEx v10, and I can see all the eQTLs in the xQTL tab. However, I'm now not able to run GENE2FUNC using the genes identified in the xQTL mapping because there are no mapped genes. I also tried to use SNP2GENE with just the legacy eQTL option, and I'm not able to submit the job without also selecting positional, xQTL or ci mapping. Many thanks in advance for your help! Andrew 

[Tanya Phung]

Hi Andrew, 

Thanks for reporting this. Sorry I made a typo in the previous fix. It should work now. In this screenshot I only selected the legacy eQTL mapping: 

Thanks for letting me know about the issue with GENE2FUNC. For now, the genes from xQTLs mapping are not included automatically to be carried over to the GENE2FUNC module. I will add this to be updated in the next release. 
For now, what you can do is to download the file and extract just the genes. Then you can upload the genes to the GENE2FUNC module manually. 

Best,
Tanya

[ANDREW MORRIS]

Thanks Tanya. All sorted now. Appreciate your help! Andrew