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Thread: Nebula Genomics (30x Whole Genome Sequencing)

  1. #51
    Advisor Jovialis's Avatar
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    Quote Originally Posted by Palermo Trapani View Post
    Jovialis: Thanks, DNA Kit Studio, is that free or need to be purchased. I was able to combine the other 2 with GEDMATCH for a Combined GEDMATCH Kit and a colleague of mine (Data analytics) used Alteryx to combine the two into a file I could use for Admixture studio. NAT GENO (I don't have the Helix version) is in a different format but might be able to get it into a format that can be combined with other two.
    Yep, DNA Kit studio is a free software.

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    Jovialis: Ok, thanks

  3. #53
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    1 members found this post helpful.
    Distance to: Jovialis_Nebula
    0.49608467 Jovialis_Superkit

  4. #54
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    Quote Originally Posted by Jovialis View Post
    Distance to: Jovialis_Nebula
    0.49608467 Jovialis_Superkit
    Could you puy in the calc all your kits just like that so we can see the distances betwen them?
    “Man cannot live without a permanent trust in something indestructible in himself, and at the same time that indestructible something as well as his trust in it may remain permanently concealed from him.”

    Franz Kafka

  5. #55
    Advisor Jovialis's Avatar
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    Quote Originally Posted by Archetype0ne View Post
    Could you puy in the calc all your kits just like that so we can see the distances betwen them?
    This is Dodecad Globe 13:

    Distance to: Jovialis:Nebula
    0.47455242 Jovialis:AncestryDNA
    0.49608467 Jovialis:Superkit
    1.18004237 Jovialis:FTDNA
    1.26751726 Jovialis:Nat_Geo_Helix_2.0
    2.21262288 Jovialis:Living_DNA
    2.36122849 Jovialis:23andme_V5

    This is Dodecad K12b:

    Distance to: Jovialis:Nebula
    0.59531504 Jovialis:Superkit
    0.77440300 Jovialis:AncestryDNA
    1.69289693 Jovialis:FTDNA
    1.75570499 Jovialis:Nat_Geo_Helix_2.0
    3.59815230 Jovialis:Living_DNA
    3.65116420 Jovialis:23andme_V5

    The distance is a lot closer than the PCA would lead me to believe.

  6. #56
    Advisor Jovialis's Avatar
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    Quote Originally Posted by Jovialis View Post
    This is Dodecad Globe 13:

    Distance to: Jovialis:Nebula
    0.47455242 Jovialis:AncestryDNA
    0.49608467 Jovialis:Superkit
    1.18004237 Jovialis:FTDNA
    1.26751726 Jovialis:Nat_Geo_Helix_2.0
    2.21262288 Jovialis:Living_DNA
    2.36122849 Jovialis:23andme_V5

    This is Dodecad K12b:

    Distance to: Jovialis:Nebula
    0.59531504 Jovialis:Superkit
    0.77440300 Jovialis:AncestryDNA
    1.69289693 Jovialis:FTDNA
    1.75570499 Jovialis:Nat_Geo_Helix_2.0
    3.59815230 Jovialis:Living_DNA
    3.65116420 Jovialis:23andme_V5

    The distance is a lot closer than the PCA would lead me to believe.
    Also interesting is that for Globe 13, the ancestry raw data is slightly closer to the Nebula sample than the superkit, despite having lower coverage. Albeit, infinitesimal, it seems the slightly higher coverage for the superkit skewed it a tiny bit. But once the rest of the coverage was met by the Nebula raw data, it pulled it back to the appropriate position.

  7. #57
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    Ancestry you meant I am sure.

    And yes that is quite interesting. Just a coincidence surely. But really puts Ancestry in a good light.

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    1 members found this post helpful.
    Filename Calculator Genotype ratio
    Merged kits.txt Dodecad K12b 97,61%

    Vahaduo Dodecad K12b updated

    Distance to Dk12ComboD
    5.49689913 Portuguese
    5.75458078 Spanish_Canarias
    6.58738188 Spanish_Castilla-Leon
    6.96282988 Spanish_Galicia
    7.28287031 Spanish_Valencia
    7.37196039 Spanish_Andalusia
    7.83413684 Spanish_Baleares
    8.22455470 Spanish_Asturias
    8.50034705 Spanish_Catalonia
    8.83516270 Spanish_Aragon
    9.50052104 Spanish_Cantabria
    10.77207501 Italian_Aosta_Valley
    11.53501192 Spanish_La_Rioja
    12.40179826 Italian_Piedmont
    12.41317496 Swiss_Italian
    12.79627289 Italian_Lombardy
    13.16973804 Italian_Trentino
    13.71645362 Italian_Liguria
    14.00724455 Italian_Veneto
    14.49210820 Italian_Emilia
    14.54362747 French_Southwest
    15.33367536 Italian_Friuli_VG
    15.88246203 Italian_Tuscany
    16.03369577 French_Corsica
    16.51399709 French_Northeast

    Target: Dk12ComboD
    Distance: 4.3568% / 4.35682776
    84.0 Spanish_Canarias
    16.0 Spanish_Basque




  9. #59
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    Can you tell what is the average number of readings for each base, how long are the base strings, and if you also received the result regarding ancestors and the microbiome in the result received?

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    Quote Originally Posted by Regio X View Post
    What read length did you get? I've seen comments that the actual read length in Nebula dropped to 100 bp, while the expected would be 150.
    BEWARE! After waiting more than 8 months and contacting the bank for a refund, I have now two results of 29X/100bp and 30X/100bp... And an other delivered after 14 months! with only 22X/150bp. All three are under 30X/150bp! No ancestry and no microbiome! And they refuse to correct the results.
    Last edited by aalexa; 11-09-21 at 08:36.

  11. #61
    Advisor Jovialis's Avatar
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    It turns out it is indeed 100 bp, I can verify.

    Nevertheless, it is still over 4 million SNPs in the raw data file, vs 1 million in the superkit.

  12. #62
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    Quote Originally Posted by Jovialis View Post
    It turns out it is indeed 100 bp, I can verify. Nevertheless, it is still over 4 million SNPs in the raw data file, vs 1 million in the superkit.
    At 30x/100bp there is a huge difference between the number of mutations reported on the Y chromosome compared to 30x/150bp as they promised. Thus at 100bp there are 6600 mutations and at 150bp there are 8310 mutations signaled in the vcf files. 25% higher at 150bp!

  13. #63
    Advisor Jovialis's Avatar
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    Quote Originally Posted by aalexa View Post
    At 30x/100bp there is a huge difference between the number of mutations reported on the Y chromosome compared to 30x/150bp as they promised. Thus at 100bp there are 6600 mutations and at 150bp there are 8310 mutations signaled in the vcf files. 25% higher at 150bp!
    Yeah, it is unfortunate that I couldn't get the 150 bp, because they made the switch.

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