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Thread: Few questions on getting started with analysis

  1. #61
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    I-L813 >Y36690

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    And what do you think of qpBound ?
    My results from David Wesolowski's Ancestry Detective Service:

    West British (Britonic?) 42.3%
    Continental Northern and Eastern European 36.6%
    Central French 21.1%

  2. #62
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    R1a > M198 > YP 1337

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    Quote Originally Posted by anglesqueville View Post
    I looked at Rarecoal more than a few minutes. Seems I lack some IQ points. That said, Beagle/FastIBD is not very easy either, to say the least. qpGraph is technically user friendly, but my feeling is that this soft is only for people with a deep knowledge of the ancient populations involved in the analyses. For a beginner, I would recommend f3, Dstat, and qpAdm in that order. A beginner should not forget smartpca. I got recently very fine and convincing results for a very specific question (chrom 6 HLA zone with the Pagani dataset) with smartpca and ( likely Chad is going to laugh) nMonte as extra tool. Anecdotally, all this together makes a not ridiculous tools bundle for amateurs ... I was recently speaking with a man who teaches genetics in a french province university ( hum... not Harvard or Cambridge) and obviously he was absolutely ignorant of all that. All he told was: "Fst", and as I had quoted several times the name of Nick Patterson, he asked: "the guy you speaks about, Nick something, who is he?"
    But it seems our forum genetic masters (Generalissimo, Vadim, Kurd, I don't know about Chad) aren't professional geneticists from universities, as far as I know. But their knowledge individually, not to say gathered together is bigger than most of academic teams specialized in population genetics. At least when I speak about Poland...
    Last edited by lukaszM; 03-30-2018 at 05:04 AM.

  3. The Following 2 Users Say Thank You to lukaszM For This Useful Post:

     Helgenes50 (03-30-2018), slievenamon (03-30-2018)

  4. #63
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    Quote Originally Posted by Helgenes50 View Post
    And what do you think of qpBound ?
    Never used it. I may of course be wrong, but I am not sure it's very useful, as you can easily compute the standard error on the D result with f3, f4 or D ( furthermore I seem to recall that there is an option in qpDstat in order to get it directly).
    En North alom, de North venom
    En North fum naiz, en North manom

    (Roman de Rou, Wace, 1160-1170)

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     Helgenes50 (03-30-2018)

  6. #64
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    Quote Originally Posted by lukaszM View Post
    But it seems our forum genetic masters (Generalissimo, Vadim, Kurd, I don't know about Chad) aren't professional geneticists from universities, as far as I know. But their knowledge individually, not to say gathered together is bigger than most of academic teams specialized in population genetics. At least when I speak about Poland...
    Don't know about Poland, but it's certainly true in France, at least in the little provincial universities. That said I don't doubt that there are in Paris or Varsovia actual specialists.
    En North alom, de North venom
    En North fum naiz, en North manom

    (Roman de Rou, Wace, 1160-1170)

  7. #65
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    R1a > M198 > YP 1337

    Poland
    Quote Originally Posted by anglesqueville View Post
    Don't know about Poland, but it's certainly true in France, at least in the little provincial universities. That said I don't doubt that there are in Paris or Varsovia actual specialists.
    I think many of them still live in Cavalli-Sforza times, of blood groups and enzimes...
    K36 Ancestry Report, map and other ancestry tools - Hidden Content
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  8. #66
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    so... qpAdm, liblapack.so.3
    It wants it, I couldn't find "liblapack.so.3" I found "liblapack.so.3.6.2" and downloaded it, now what? I put it in the directory qpAdm is in but it doesn't acknowledge. I tried renaming it just for fun, still nil.
    PM me for d-stats. If I have the samples I will run them. Also, here is a collection of 14,000. Part 1: Hidden Content Part 2: Hidden Content Part 3: Hidden Content Looking for: Tianyuan and Sunghirs in plink/eigenstrat, 1240k snp panel

  9. #67
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    Quote Originally Posted by Kale View Post
    so... qpAdm, liblapack.so.3
    It wants it, I couldn't find "liblapack.so.3" I found "liblapack.so.3.6.2" and downloaded it, now what? I put it in the directory qpAdm is in but it doesn't acknowledge. I tried renaming it just for fun, still nil.
    Make sure you have internet connection and input:

    sudo dnf install liblapack-dev

    Depending on speed it should take 15-40 minutes. I have to do this everytime I run qpAdm from live usb. For me it actually downloads 8 packs, including blas.

  10. #68
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    Aww that's dumb, I didn't think Linux 'installed' a lot of things. I'll have to hook my Linux comp to the web tomorrow. If I can get it to work without having to install every time, feel free to send me any qpAdm runs you want Bas and I'll do them, you've been so much help
    PM me for d-stats. If I have the samples I will run them. Also, here is a collection of 14,000. Part 1: Hidden Content Part 2: Hidden Content Part 3: Hidden Content Looking for: Tianyuan and Sunghirs in plink/eigenstrat, 1240k snp panel

  11. #69
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    Interesting fact to note in the event someone else has this problem.

    You can't run qp3pop F3's with a target that is a single individual. If you have inbreeding off (default) the SE will be in the trillions, if inbreeding is on, the result is 'no data'.

    EDIT: I think liblapack was updated or something, the command that worked (for Fedora25 at least)

    sudo dnf install lapack
    Last edited by Kale; 04-21-2018 at 07:22 AM.
    PM me for d-stats. If I have the samples I will run them. Also, here is a collection of 14,000. Part 1: Hidden Content Part 2: Hidden Content Part 3: Hidden Content Looking for: Tianyuan and Sunghirs in plink/eigenstrat, 1240k snp panel

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