kyoko-wtnb / fuma-webapp Goto Github PK

Dear All,
Thanks for the great tool. I would like to add the tools for manhattan and Q-Q plot as command-line executables in the next flow pipeline I am developing. I am was searching through the storage/scripts folder for that, however, I am not able to find script which is directly plotting the manhattan plots and Q-Q plots. It would be really great if you could provide the scripts for generating the plots so that I can add them as part of the pipeline.
Thanks

Hi,

I have been working on trying to replicate the whole FUMA-webapp on my local PC and am able to get the front end of the app running and I am facing a few issues.

1. By default, every run creates a folder in the root "/jobs/1", after going through the multiple config files, I identified that in the sessions.php inside the config folder we can change the path variable from "/" to any other folder, with write permissions but it seems it is still trying to save it in the root "/jobs/" folder. The workaround for was to run the server as root.

2. Once I got it up and running as root, when I tried to run an example file, the process throws an error regarding the config file (/FUMA-webapp/storage/script/app.config) that needs to have the pointers to where all the different tools and databases need to be stored. Could you please mention share the versions of tools and databases used in the online webapp, so as that the results would be consistent.

I try to run scripts of FUMA in my server, but I meet some problems.

In scripts/magma.py, whether magma param --gene-loc "+magmafiles+"/ENSG"+ensg_v+".coding.genes.txt" is from https://www.dropbox.com/s/ok8b67i9qf3jt2y/ENSG.tar.gz

The files annotfile = annot_dir+"/chr"+str(chrom)+".annot.gz" mentioned in scripts/getLD.py file cannot be found.

I would be appreciated it if you offer me the code to generate these files.

best regrads,
meng

H-MAGMA https://doi.org/10.1038/s41593-020-0603-0
eMAGMA https://doi.org/10.1101/854315
Enhancer to Gene connections https://doi.org/10.1101/2020.09.01.278093
RegulomeDB v2.0 https://regulomedb.org/regulome-search
SynGO annotations https://doi.org/10.1016/j.neuron.2019.05.002

Hi,

I would like to run the FUMA-webapp in a docker container.
Do you have any tipps to achieve this ?
Is there any detailed documentation about the web-app and its files?

Best regards,

Farid

Dear FUMA team,

I have been trying to open FUMA to download my results and the site cannot be reached. I tried reaching from different computers and networks without any success. Is it a server issue? Please revert back soon.

Thanks and Regards,
Janaki Nair

Hi @Kyoko-wtnb,

Seems like https://fuma.ctglab.nl/ is not accessible (at least from Hungary), this problem is a few weeks old.
We tried to access it from different computers and different networks (both university and home networks), without success, the connection times out.
Maybe a server hosting issue?

Kind regards,
Tamás

Dear Fuma team,

I am wondering whether FUMA accept hg38 based GWAS summary statistics?

Thanks

Shicheng

Hi,

I am wondering which LD parameter is used in the eQTL mapping? SNPs in LD with the lead SNP in GWAS locus are included and mapped with eQTL data. Is the LD threshold here a user-specific one (i.e., the same as clumping analysis) or a value by default?

Thanks!

Hi, it would be nice to add option to only label leading SNPs with an option to select threshold (in SNP2GENE section, in the "Mahattan Plot (gene-based test)")

Hi, Previously I have user FUMA a little bit, by submitting my GWAS to the FUMA web server.
And I have been wishing that you guys could release a version that I could install locally.

So, is FUMA-webapp something that I have been hoping for, something that I could download and set up and run on my local computer? That would be really awesome!

Best regadrs,
jie

Dear Kyoko:

I am trying to re-learn FUMA, through the example BMI GWAS descirbed in your Nature Communications paper.

1. The paper says that "We first conducted positional mapping of deleterious coding SNPs and eQTL mapping which prioritized 151 unique genes; ... 144 genes with eQTLs that potentially alter expression of these genes." Below is the screenshot of the 144th eQTL, sorted by P-value. I could not see what threshould is used to come up with 144 genes.

2. Does FUMA pick eQTL genes regardless of tissue types, even though some tissue types might have nothing to do with BMI? Below is the plot for eQTL. Why there are "GTEx v6 30 general tissue types" since there is already "GTEx v6 53 tissue types"? I though that the latter already included the former. Previously I used FUSION/TWAS to run similar analyses and generated similar plots. So, my question is, does the eQTL mapping of FUMA similar as that of FUSION/TWAS?

3. The paper says that "“The 400 prioritized genes showed enrichment in 9 GO terms". I do see there are 5 signals from WikiPathways, isn't that worth mentioning? For one GWAS that I run on FUMA, I see 58 Go biological processes and 4 GO molecular functions, besides 4 cancer gene modules, etc. So, this is way too much to summarize. Don't know if you got a recommendation here on which results worth reporting.

4. I noticed a new “Cell Type” menu is added to FUMA. Is that something not available in GENE2FUNC? It would be great to run this analysis for the example BMI GWAS, so that users get a clear idea on what it is about and what the analysis output looks like.

This is all my questions.

Thank you very much & best regards,
jie

Dear FUMA team,

I want to use FUMA on my trans-ancestry GWAS. There is an issue that the LD map for trans-ancestry analysis is calculated a weighted LD value by the sample size of each population. But I can't predefine the LD map in FUMA or calculate the new LD map by the sample size. How can I solve this problem? OR how can I change the script to import my own LD map to identify the lead SNPs and locus (this is my main purpose)?

Thanks and Regards,
Yun Luo

Hi,

I want to ask where are the scripts to query a list of SNPs from my study on CATALOG GWAS?
I am doing it now manually on the GWAS CATALOG web page, but I assume that FUMA does it with scripts. I found a python script in your repo: getGWAScatalog.py

But the code does not work. Can you elaborate more on this?

Thanks

Hi @Kyoko-wtnb,

Thanks for a great app!

You mentioned in #1 that you wanted to create a separate repository only for the main process of the FUMA. Is there any update on this?

Also, is there any way that I can download the resources in app.config eg the ENSG data: /data/ENSG.file.txt (I think it's data from Ensembl for GRCh37 v92).
I have had a look at the links but couldn't find the data.

Thanks in advance

It seems https://fuma.ctglab.nl is currently not reachable.

Are the genes.raw files available from your magma output/gwas atlas? they would be useful.

I come from China, I am using the FUMA for gene set enrichment, but FUMA not respond to my uploaded gene list (I tried to ENSEMBL ID/gene symbol). What is wrong has happened? Is FUMA running well now?

Hallo,

I am trying to delete some jobs by selecting the delete button but it seems it is not removing selected jobs.

Hi Kyoko,

I'm unable to download any of the results files from GENE2FUNC.

When I click on the download image, I get the following error message:

Whoops, looks like something went wrong.

ImagickException in FumaController.php line 380:
no decode delegate for this image format `SVG' @ error/blob.c/BlobToImage/361

I appreciate it if this can be fixed ASAP. TIA
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