Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
  • Jul 26 09:20

    tsujigiri on genomeprep

    (compare)

  • Jul 26 09:20

    tsujigiri on master

    add genomeprep link (#538) (compare)

  • Jul 26 09:20
    tsujigiri closed #538
  • Jul 25 12:45
    gedankenstuecke commented #538
  • Jul 25 11:54
    tsujigiri synchronize #538
  • Jul 25 11:54

    tsujigiri on genomeprep

    Run DatabaseCleaner before RSpe… Merge branch 'master' into geno… (compare)

  • Jul 25 09:02

    gedankenstuecke on setup-github-action

    (compare)

  • Jul 25 09:02

    gedankenstuecke on master

    Run DatabaseCleaner before RSpe… (compare)

  • Jul 25 09:02
    gedankenstuecke closed #539
  • Jul 25 07:44
    tsujigiri commented #538
  • Jul 25 07:43
    tsujigiri opened #539
  • Jul 25 07:41

    tsujigiri on setup-github-action

    Rename workflow Run DatabaseCleaner before RSpe… Run on all pushes (compare)

  • Jul 25 07:37

    tsujigiri on setup-github-action

    fixup! Run DatabaseCleaner befo… (compare)

  • Jul 25 07:35

    tsujigiri on setup-github-action

    Run on all pushes (compare)

  • Jul 25 07:28

    tsujigiri on setup-github-action

    Run on all pushes (compare)

  • Jul 25 07:22

    tsujigiri on setup-github-action

    Run tests on GitHub WIP Update mimemagic and rails gems and 34 more (compare)

  • Jul 25 06:31
    philippbayer commented #538
  • Jul 24 12:59
    gedankenstuecke synchronize #538
  • Jul 24 12:59

    gedankenstuecke on genomeprep

    Run tests on GitHub (#536) * R… Merge branch 'master' into geno… (compare)

  • Jul 24 12:59

    gedankenstuecke on setup-github-action

    (compare)

Mark Glasgow
@glasgowm148
Is there an easy way to export everyone who has a specific mutation?
Philipp Bayer
@philippbayer
sadly not right now! you can export all specific phenotypes, but not specific snps
you could download the entire dataset and use grep to find the right files
philiprhoades
@philiprhoades
People,
I signed up here some time ago but never got around to doing anything interesting with my (and my parents and two siblings) 23andMe stuff past doing a Promethease report as well. Now one sibling wants to extend the testing to her children and some in-laws. There seems to be some hassle with people ordering on 23andMe from Australia now so I went looking at the alternatives - overall, MyHeritage appears to be the best combo of Genetics and Genealogy choice - do people here have preferences / suggestions? It would be nice if openSNP had grown to the scale of some of the commercial ops DBs . . but I guess that is not the way of the world . .
Thanks,
Phil.
Philipp Bayer
@philippbayer
I think here in Australia, ancestry.com is the biggest provider? at least the one that advertises the most :) they give you your raw data too: https://support.ancestry.com.au/s/article/Downloading-AncestryDNA-Raw-Data
'professional' projects like dna.land and others who have proper staff etc. have grown relatively large, and I'm happy with them :) I think we'd struggle a lot (computationally) if we'd work on that scale
Bastian Greshake Tzovaras
@gedankenstuecke
yep, if we’d grow to the size of those companies we’d be in real trouble in terms of scaling our system :D
philiprhoades
@philiprhoades
Philipp and Bastian,
Right - thanks for that.
Bastian Greshake Tzovaras
@gedankenstuecke
MyHeritage is pretty big these days too and my best guess is that it doesn’t really make a big difference which provider you go with as the data is pretty similar across all of them
philiprhoades
@philiprhoades
Right - good to know.
Bastian Greshake Tzovaras
@gedankenstuecke
I know that MyHeritage allows the upload of data from other providers
I’m not sure whether Ancestry allows that too
Philipp Bayer
@philippbayer
probably not from looking through their faq, no mentinos
philiprhoades
@philiprhoades
Yes, I just tested that as an exercise with MyHeritage - it took them a few days to process the 23andMe file and I got a bit of info back but to get all of the info they want to charge another AUS$48 . .
It looks like we might stick with 23andMe just for the convenience of most of the family already being there . .
Bastian Greshake Tzovaras
@gedankenstuecke
yeah, that certainly makes things easier if you already have many people on 23andme
Philipp Bayer
@philippbayer
makes sense to me!
Bastian Greshake Tzovaras
@gedankenstuecke
and i just uploaded my own 23andme data to myheritage just for fun, to see what they offer :)
philiprhoades
@philiprhoades

I know what you mean about scaling and processing but for some years I have been following:

https://safenetwork.org

which could potentially offer a distributed store of data and possibly processing . . it would be great to have an inexpensive store and comparison of nearly ALL the data from the commercials . .

Philipp Bayer
@philippbayer
currently we're still ok (thanks to patreon!!) but it could be a thing for the future!
philiprhoades
@philiprhoades
There is a bunch of stuff I want to put there once they go live - I will keep this stuff in mind and bring it up again in the future . .
Bastian Greshake Tzovaras
@gedankenstuecke
thanks!
Philipp Bayer
@philippbayer
Bastian Greshake Tzovaras
@gedankenstuecke
wow!
Bastian Greshake Tzovaras
@gedankenstuecke
420 and me! :D
Philipp Bayer
@philippbayer
I didn't see that dna.land is closing down/relaunching as a commercial service? https://medium.com/@dl1dl1/dna-land-is-relaunching-34f5a505504f
Philipp Bayer
@philippbayer
I like this: 'Please note that because DNA.Land is closing as a research project, all accounts and data will be permanently deleted and erased from the DNA.Land servers on September 30th, 2019. You will be able to recreate an account on DNA.Land 2.0 and upload your data just as you did when you signed up to join DNA.Land.'
Bastian Greshake Tzovaras
@gedankenstuecke
@philippbayer yeah, that’s cool. I had missed that somehow!
Philipp Bayer
@philippbayer
updating ssl certificate right now, server seems to have trouble coming back
oh. the harddrive is full\
Philipp Bayer
@philippbayer
ok fixed, for now
Bastian Greshake Tzovaras
@gedankenstuecke
whops :D
i think our automated cleanup of older zip archives doesn’t work, that’s why it just keeps adding them :D
Paweł Olszewski
@olszewskip
Hi, hello!
I'm interested in doing some genome-wide, "population-long" association studies between genotypes and phenotypes, with the motivation being just self-education and training in this sort of analyses, trying out different statistics and algorithms etc. First I was planning on simulating data with HAPGEN2, but then I stumbled upon openSNP. I was wondering if You know of any existing projects that use openSNP data for discovering phenotype associations? Also, maybe You can recommend any software tools for converting the genotypes from openSNP into a uniform file format, like VCF?
Bastian Greshake Tzovaras
@gedankenstuecke

hey @olszewskip! There was one crowdsourced AI challenge done with the data that would fit your description: https://www.crowdai.org/challenges/opensnp-height-prediction

They also created an open source pipeline to prepare the data from openSNP for the challenge: https://github.com/onaret/opensnp-cohort-maker

Paweł Olszewski
@olszewskip
Awesome! Many thanks.
Bastian Greshake Tzovaras
@gedankenstuecke
And if you want to use plink for the GWAS: They actually have a function to convert 23andMe files to the input plink needs
Paweł Olszewski
@olszewskip
Nice, I was vaguely aware of that, but I haven't yet had a chance of working with any 23andMe files. Does it make sense to use plink not only for GWAS'es but also simply for 23andMe -> VCF conversion?
Bastian Greshake Tzovaras
@gedankenstuecke
iirc plink doesn’t use VCF files but their own, more simple format. I think @philippbayer knows more about that though
Paweł Olszewski
@olszewskip
Sadly I cannot access the data prepared by crowdai without an account, and I cannot sign up because apparently the site is shutting down and not allowing new sign-ups :( If anyone knows of any way that I could still access that AI challenge data, please let me know.
Bastian Greshake Tzovaras
@gedankenstuecke
I’d try emailing them if there’s a contact email
@olszewskip if there’s no email around let me know and i’ll look through my archives and find it
Paweł Olszewski
@olszewskip
Sylvain Bernard from EPFL has kindly provided me with the data. Many thanks, @gedankenstuecke
Bastian Greshake Tzovaras
@gedankenstuecke
yay, that’s great! :)
alcogni
@alcogni
@gedankenstuecke I downloaded some phenotypes and genotypes included sometimes belongs to users either not at openSNP website anymore or the user number at website and user number at genotype are different. Could you please help me to understand.
JialinKang
@JialinKang
hi, the website opensnp.org is broke.
Helge Rausch
@tsujigiri
Oops... You are right! 🔎
Bastian Greshake Tzovaras
@gedankenstuecke
@JialinKang thanks to @tsujigiri the site is back up 💖
marcushdawson
@marcushdawson
Hi, I am getting "404: Whatever you tried to access is not here." message when trying to download all data from OpenSnp
Bastian Greshake Tzovaras
@gedankenstuecke
hey @marcushdawson, thanks for letting us now! I think there was an issue with creating the latest version of the archive and I’ve already kicked the machine and restarted the job. So hopefully at the end of the day there should be a new one :)