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@forestglip which software did you try to FINEMAP with? Haven’t had time to setup the virtual machine today, but looking over FINEMAP vs SUSIE R

Alright I got POPs to run but unsure if some of the parameters I used are correct. The setup: Cloned https://github.com/FinucaneLab/pops , then setup a virtual env using python 3.8 (it needs this for some of it's dependencies), installed requirements.txt in this env I then created a folder in...

Found it in the public, not sure why link was not working. Looks like I needed the "browse" portion in the url https://fuma.ctglab.nl/browse/653365

Oddly it's still saying restricted

Any chance your FUMA run was public? Not that I don't trust you but downloading then running zips feels a bit sketchy haha I couldn't find your run here: https://fuma.ctglab.nl/browse

@forestglip Hey, if you have a chance could you see if there is magma.genes.raw as well? POPs needs this file as well. The Magma should have created this

Looking at his github he has two repositories doing two things: DecodeMe - this looks like to me additional statistics that does fine mapping on only lifted over DecodeMe data. Which leads me to believe something when wrong with his lift over/munging "This analysis generates two supplementary...

I think we've talked about this before, but it’s always interesting how our stories are nearly identical. Strep infection that did not clear, sat with the infection for over a week, then month later led to ME/CFS, started with unrefreshing sleep. I got those white tonsils for my first 3 years...

Is this relevant now that DecodeME has a lot of brain tissue hits

Alright next problem, I see why Paolo has munged/lifted over. This tool only uses hg19 where DecodeME is hg38. We need hg19, so the liftover was necessary: https://groups.google.com/g/fuma-gwas-users/c/E4BeXe8vox0 "Of course there will be some loss of variants due to the conversion not being...

Sorry have not had as much free time to work on this. I think my next step is to tackle step 1 & step 2, which can be done through the online tool: https://fuma.ctglab.nl/ Interestingly I see Paolo has already done this with "munged" ( GRCh38 reference genome, which the original DecodeME data...

Has anyone compared the genes he has highlighted here to the genes in the decodeMe Magma?

Hmm I’m more interested in just running FLAMES on only the decodeME data. I’m not so up to date but i believe this is the highest quality of GWAS data, and want to see what the FLAMES analysis provides more clues. Still interesting work! Does he have any interest in joining this forum or...

I read some of Paolos blog, sounds like he is worse in winter :( if it’s too much I would rather not bother him. I’ll start a google collab tonight. I’m happy to coordinate on here or start a small discord server, up to y’all.

Thinking about it I could probably host it on a google collab notebook if I pay for a little storage.

My fear as well. I’m hoping by documenting my steps extremely clearly I can at least have others replicate and potentially check my work. It’s more the biology decisions of the data and lift overs that worry me. Dropping something without having the correct translation. I’ll try to outline my...

Update for my work tonight, I got a new PC so had to rebuild the environment. Rebuilt and got the example data working. Interesting I was looking to accomplish step 1 & 2 and found some has already done most of the work! https://github.com/paolomaccallini-hub/DecodeME Anyone in contact with...

Hi all, Something that has been in the back of my head since the DecodeME data was released was running the newer FLAMES analysis: https://github.com/Marijn-Schipper/FLAMES Somewhat discussed here...

I’ve wonder if there have been studies on cytochrome P-450 enzymes in relation to ME/CFS. That would be a good place to start if think

What’s the timeline on the F&M Dara trial, it already started? Anywhere they post updates, not results, just how far along they are with dosing/how many ppl processed?