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Thread: cartes "Multidimensional Scaling" pour génomes diploïdes

  1. #121
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    Quote Originally Posted by Finn View Post
    Sorry for not making it very clear. But what is de advantage of this type of files (i can't imagine another word now) above the usual ones?
    I'm assuming you're referring to the adjective "diploid" in reference to the title? But these are the usual genomes. The others are the pseudo-haploid genomes used by Reich and all his followers for old data and too poor to allow reading of the two alleles. If I specified in my title, it is so that I'm not asked to integrate old genomes, which I do not know how to process by this method.
    En North alom, de North venom
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  3. #122
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    Finn: teasing: I just finished the imputation of 149 Dutchies with regional specifications. Don't rejoice too quickly, these are very poor genomes and I'm really wondering what my imputation pipe-line has given on such a difficult basis. Wait and see, haha!
    En North alom, de North venom
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  5. #123
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    Quote Originally Posted by anglesqueville View Post
    Finn: teasing: I just finished the imputation of 149 Dutchies with regional specifications. Don't rejoice too quickly, these are very poor genomes and I'm really wondering what my imputation pipe-line has given on such a difficult basis. Wait and see, haha!
    That's very interesting Angles!!

    There are 165.000 North Dutch samples there, but I guess only available for (health) research:
    https://www.lifelines.nl/researcher/...iobank/genomic

    But how about this one (also connected to this research of Life Lines)
    http://www.nlgenome.nl/?page_id=9

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  7. #124
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    Quote Originally Posted by Finn View Post
    That's very interesting Angles!!

    There are 165.000 North Dutch samples there, but I guess only available for (health) research:
    https://www.lifelines.nl/researcher/...iobank/genomic

    But how about this one (also connected to this research of Life Lines)
    http://www.nlgenome.nl/?page_id=9
    Forget my teasing. I wasted my time, as these genomes happen to be pseudo-haploid ones. I was aware of that, why did I forget and nearly burnt my PC in this job? About nlgenome, I am unable to use snv-data. And people from GoNL don't want to share their files.
    En North alom, de North venom
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    (Roman de Rou, Wace, 1160-1170)

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  9. #125
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    Quote Originally Posted by anglesqueville View Post
    Forget my teasing. I wasted my time, as these genomes happen to be pseudo-haploid ones. I was aware of that, why did I forget and nearly burnt my PC in this job? About nlgenome, I am unable to use snv-data. And people from GoNL don't want to share their files.


    I will mail you because I once had contact with the guys working in the UMCG about this.....

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  11. #126
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    Finn, perhaps I can still give you the MDS card extract for the Dutch only. Keep in mind that I don't have a clue about the consistency of these imputed haploid genomes.

    dutch_mds_1-2.pdf
    En North alom, de North venom
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    (Roman de Rou, Wace, 1160-1170)

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  13. #127
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    Quote Originally Posted by anglesqueville View Post
    Finn, perhaps I can still give you the MDS card extract for the Dutch only. Keep in mind that I don't have a clue about the consistency of these imputed haploid genomes.

    dutch_mds_1-2.pdf
    Nice!
    Ok the input is questionable but about the outcome: I did a quick scan, with some common sense, I would say it could be quite right......

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  15. #128
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    Quote Originally Posted by Finn View Post
    Nice!
    Ok the input is questionable but about the outcome: I did a quick scan, with some common sense, I would say it could be quite right......
    I won at least one thing: a hard session of imputation training. Good Gracious, how I hate this work... I'm never sure that what I'm doing is right and there are many points that I understand only partly. I tried yesterday to impute the 21 Germans from Karafet: no way, I was unable to align the genomes to the references. Why? No idea. It's really frustrating. The only thing that reassures me a little: I'm not the only zero in this matter, the Internet is full of guys who are lost in imputation and cry for help.
    En North alom, de North venom
    En North fum naiz, en North manom

    (Roman de Rou, Wace, 1160-1170)

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  17. #129
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    Je sors de deux rounds d'imputation "en masse" sur la base de fichiers 23&me sortis des bas-fonds de mes disques durs externes (incl. des ftdna convertis). Je crois que je maîtrise maintenant ce pipe-line sur ce type de données, pénible du fait de nombreuses choses "sales" (SNPs flippés, indels, etc). J'ai évidemment fait subir aux données post-imputation l'épreuve du MDS, et je crois que je vais m'offrir un whisky ce soir pour me récompenser. Je suis vraiment content, parce que ce n'était pas gagné.

    D'abord des données que je croyais avoir perdues depuis longtemps, enfermées dans un répertoire "ffoucart", bien que 2 individus soient, ou mal étiquetés, ou inconnus. Je ne vais pas poster les 10 MDS, seulement ceux de l'ami Foucart (cherchez "ff") de sa compagne Isaure (cherchez "ff_isaure"), et de son père (ff_jeanpaul). Il rectifiera si je me trompe, mais je crois que tout ce monde-là est de la région Nord, avec de profondes racines flamandes. MDS les localise à la lisière de la zone CEU/GB, dans une région qui serait à coup sûr occupée par les Allemands si j'en avais plus que 3 (2 des 3 Allemands d'EGDP y sont).

    ff_mds_1-2.pdf
    isaure_mds_1-2.pdf
    jeanpaul_mds_1-2.pdf

    Ensuite des données que j'ignorais avoir, parmi lesquelles celles de notre ami celticgerman, d'un de ses amis (ou relatifs) étiqueté "germandane" (Allemand du nord):
    celticgerman_mds_1-2.pdf
    germandane_mds_1-2.pdf
    En North alom, de North venom
    En North fum naiz, en North manom

    (Roman de Rou, Wace, 1160-1170)

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  19. #130
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    Enfin les données de deux autres amis forumers, vettor et vestri:

    vettor_mds_1-2.pdf
    vestri_mds_1-2.pdf

    Voilà. Les fichiers imputés par mes soins comptent autour de 30 millions de SNPs, contre les 40 de dna.land (de mémoire). Sur ces 30 millions, et sur les cas que j'ai testés, la coïncidence avec l'imputation dna.land n'est jamais inférieure à 99%. Ce n'est pas extraordinaire, mais ce n'est pas mal. Si vous en avez marre d'attendre le réveil de dna.land, vous pouvez m'envoyer des données de compagnies (23&me seulement svp, convertissez les autres), mais sachez que comme j'impute par paquets de 10 (ou plus), je ne ferai pas tourner la machine pour une personne isolée, donc il risque d'y avoir là aussi un temps d'attente.
    En North alom, de North venom
    En North fum naiz, en North manom

    (Roman de Rou, Wace, 1160-1170)

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