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Thread: Salmonella enterica from a soldier from the 1652 siege of Barcelona (Spain) supports

  1. #21
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    Quote Originally Posted by Michalis Moriopoulos View Post
    Yeah, that's a strange screw-up on the authors' part. Wonder what the discrepancy is here.
    I tried to model him to see if we can detect a sardinian contribution (if mixed), but nothing at all, he is indeed a Spaniard.


    Distance :

    0.03591165 Spanish_Penedes:VID003
    0.03639279 Spanish_Valencia:ALB126
    0.03676528 Spanish_Camp_de_Tarragona:GRA011
    0.03721441 Spanish_Andalucia:AND46
    0.03731811 Portugueseortugal2
    0.03744975 Spanish_Alacant:NAC135
    0.03757988 Portuguese:EBC_Portugal11
    0.03812439 Spanish_Andalucia:AND80
    0.03851019 Spanish_Camp_de_Tarragona:FOR067
    0.03879578 Portuguese:EBC_Portugal1
    0.03882284 Spanish_Castilla_Y_Leon:HG01500
    0.03927802 Spanish_Galicia:GAL35
    0.03956284 Spanish_Galicia:GAL21
    0.03961493 Spanish_Galicia:HG01686
    0.03964931 Spanish_Castilla_Y_Leon:HG01501
    0.03980113 Spanish_Baleares:HG01615
    0.03983999 Spanish_Galicia:GAL74
    0.03995167 French_Occitanie:T_7
    0.03997258 Spanish_Alacant:MAS064
    0.04019241 Spanish_Cataluna:HG01537
    0.04064669 Portuguese:EBC_Portugal9
    0.04092034 Spanish_Pirineu:CAR212
    0.04099377 Spanish_Galicia:GAL3
    0.04101471 Spanish_Valencia:FER097
    0.04110478 Spanish_Andalucia:AND14

  2. #22
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    not in on the joke
    as i understand it they resampled the sardinian in 'october' with no contamination and better coverage and that proper sample plots right next to the sardinian cluster ...falling close to the genetic diversity observed in present day Sardinians...
    now how does G25 converts that fact
    GENO2.0 51SEURO 19WCEURO 13SCANDINAVIA 5ASIAMINOR 4EEURO 4GB/IRELAND 3ARABIA myOrigins 26ITA.PEN. 13GREECE&BALKANS 12SARDINIA 18GREATBRITAIN 14IRELAND 10C.EUROPE 8SCANDINAVIA DNA.Land 49NWEURO 27SEURO 13MED.ISLANDER 11SARDINIAN myHeritage 51.8NWEURO 33.2ITALIAN 7.9GREEK/S.ITALY 7.1BALKAN gencove 29NITALY 19EMED 15NBRITISLES 12SWEURO 10NCEURO 9SCANDINAVIA 6NEEURO GenePlaza 54.4NWEURO 37.6GRE/ALB 5.6WASIAN 2.4SWASIA LivingDNA 57.4S.GER 3.3NE.GER 25.8N.ITA 5S.ITA 4.3TUSCANY 2.5CYPRUS 1.7AEGEAN

  3. #23
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    Quote Originally Posted by alexfritz View Post
    not in on the joke
    as i understand it they resampled the sardinian in 'october' with no contamination and better coverage and that proper sample plots right next to the sardinian cluster ...falling close to the genetic diversity observed in present day Sardinians...
    now how does G25 converts that fact
    It could also be that teepean47 got the wrong sample (that it downloaded another one)!

    I don't know, it's hard to say.

    I know however that the PCA of the study does not correspond to the PCA of the Global 25, so either the "Sardinian" sample aka F1691_1810 is not the one that Teepean47 downloaded and hosted, or it comes from the Global 25, from the conversion .

    The position of the "Sardinian" sample of the study is located in a different cluster than the current sample that teepean47 downloaded.




    Global 25 PCA




    A person who participated in the study (Lucy Von Dorp) told me:

    "The ftp file for the Basque starts with L017 and there are multiple files for the Sardinian starting with L014 (October and April). Please note if you use the column selection and select Sample_alias and/or Sample_title, the name of each sample will be displayed."

    Antonio de Dios :

    "The original files of the Sardinian individual were splitted because of logistics reasons, but all of them (L014) are from the same individuals."

  4. #24
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    Quote Originally Posted by Olymp View Post
    It could also be that teepean47 got the wrong sample (that it downloaded another one)!

    I don't know, it's hard to say.

    I know however that the PCA of the study does not correspond to the PCA of the Global 25, so either the "Sardinian" sample aka F1691_1810 is not the one that Teepean47 downloaded and hosted, or it comes from the Global 25, from the conversion .

    The position of the "Sardinian" sample of the study is located in a different cluster than the current sample that teepean47 downloaded.




    Global 25 PCA




    A person who participated in the study (Lucy Von Dorp) told me:

    "The ftp file for the Basque starts with L017 and there are multiple files for the Sardinian starting with L014 (October and April). Please note if you use the column selection and select Sample_alias and/or Sample_title, the name of each sample will be displayed."

    Antonio de Dios :

    "The original files of the Sardinian individual were splitted because of logistics reasons, but all of them (L014) are from the same individuals."
    I downloaded all of the files (April & October) for the Sardinian individual, merged them and aligned them. I'll do it again with just the October ones.

  5. The Following 2 Users Say Thank You to teepean47 For This Useful Post:

     Michalis Moriopoulos (09-21-2021),  Olymp (09-21-2021)

  6. #25
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    Quote Originally Posted by teepean47 View Post
    I downloaded all of the files (April & October) for the Sardinian individual, merged them and aligned them. I'll do it again with just the October ones.
    All these files for a single sample can only lead to confusion.

    I think it's very easy to get lost in all of this.

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    Quote Originally Posted by Olymp View Post
    It could also be that teepean47 got the wrong sample (that it downloaded another one)!

    I don't know, it's hard to say.

    I know however that the PCA of the study does not correspond to the PCA of the Global 25, so either the "Sardinian" sample aka F1691_1810 is not the one that Teepean47 downloaded and hosted, or it comes from the Global 25, from the conversion .

    The position of the "Sardinian" sample of the study is located in a different cluster than the current sample that teepean47 downloaded.




    Global 25 PCA




    A person who participated in the study (Lucy Von Dorp) told me:

    "The ftp file for the Basque starts with L017 and there are multiple files for the Sardinian starting with L014 (October and April). Please note if you use the column selection and select Sample_alias and/or Sample_title, the name of each sample will be displayed."

    Antonio de Dios :

    "The original files of the Sardinian individual were splitted because of logistics reasons, but all of them (L014) are from the same individuals."
    Even the position of LAR017 on the G25 PCA plot seems a bit weird.

  8. The Following User Says Thank You to LesPoilus For This Useful Post:

     Olymp (09-21-2021)

  9. #27
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    Quote Originally Posted by LesPoilus View Post
    Even the position of LAR017 on the G25 PCA plot seems a bit weird.
    L017 has only one file at ENA. I processed it with eager and the results are what they are. I used bwa aln + pileupCaller with the default options so anyone else wants to process these samples is free to do so.

    EDIT: Latest version of eager that I use currently.

    https://github.com/nf-core/eager/releases/tag/2.4.0

  10. #28
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    I think LAR017 was a Basque or from the vicinity of Basque-inhabited lands.

  11. #29
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    Quote Originally Posted by teepean47 View Post
    L017 has only one file at ENA. I processed it with eager and the results are what they are. I used bwa aln + pileupCaller with the default options so anyone else wants to process these samples is free to do so.

    EDIT: Latest version of eager that I use currently.

    https://github.com/nf-core/eager/releases/tag/2.4.0
    To be clear, i was not complaining about your work. Actually, i am rather thankful to you because i do not know how to process the file(s) myself.

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     teepean47 (09-21-2021)

  13. #30
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    Quote Originally Posted by Tomenable View Post
    I think LAR017 was a Basque or from the vicinity of Basque-inhabited lands.
    He seems to be a French Basque. I found his position weird on the G25 pca plot, because i thought he was part of Sardinian ancestry.

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