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Thread: Conversion request for some novel African sample for the G25

  1. #1
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    Conversion request for some novel African sample for the G25

    Guys, I've noticed the samples used in this study Along the Indian Ocean Coast: Genomic Variation in Mozambique Provides New Insights into the Bantu Expansion. are publicly available and I think any African variation would be a welcome addition to the G25. Unfortunately still waiting on access requests for the High Levels of Genetic Diversity within Nilo-Saharan Populations: Implications for Human Adaptation study. Anyway are these the appropriate data that can be converted[?] into the appropriate format for the G25 and would someone with the relevant expertise be kind enough to do so?

    They can be found here.

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     loxias (09-21-2020),  Pedro Ruben (09-19-2020)

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    Nobody?

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    I’d help if I knew how. I’m honestly not sure how many people here actually know how to produce G25 coordinates
    distance%=4.6465"
    Barcin_N,47.2
    Yamnaya_Samara,41.4
    WHG,10.6
    Ethiopia_4500BP,0.8


    E-V13 => E-PH1246 => E-BY14160
    Antonio Reale born circa 1710, Ciminà (RC) Italy

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     ThaYamamoto (09-21-2020)

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    Quote Originally Posted by digital_noise View Post
    I’d help if I knew how. I’m honestly not sure how many people here actually know how to produce G25 coordinates
    Thanks I appreciate the sentiment man Actually all I'm asking is for someone to convert the available data into a format Generalissimo can upload to the G25, I've seen quite a few users do the very same for ancient sample data around the forum. Unfortunately can't seem to get their attention or maybe it requires too much time/leg work.

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     digital_noise (09-21-2020)

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    OK last request before I give up , mods delete this thread please in a day or two. Unfortunately can't get any luck.

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    Ask Generalissimo

    Apparently they ARE in binary ped format so they should be no trouble. I believe this is the format he works with.
    https://www.ebi.ac.uk/arrayexpress/e...-8450/samples/
    Processed data has the plink format.
    Last edited by Norfern-Ostrobothnian; 09-21-2020 at 04:45 PM.

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     ThaYamamoto (09-21-2020)

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    Quote Originally Posted by Norfern-Ostrobothnian View Post
    Ask Generalissimo

    Apparently they ARE in binary ped format so they should be no trouble. I believe this is the format he works with.
    https://www.ebi.ac.uk/arrayexpress/e...-8450/samples/
    Processed data has the plink format.
    Oh I didn't realise, I asked him a few months ago and they weren't right, I guess they might have added these recently. I'll drop him a message, thanks man. Although I think maybe he wanted them all in one file or merged I can't quite remember.

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    Quote Originally Posted by ThaYamamoto View Post
    Oh I didn't realise, I asked him a few months ago and they weren't right, I guess they might have added these recently. I'll drop him a message, thanks man. Although I think maybe he wanted them all in one file or merged I can't quite remember.
    I can merge them if he wants them merged

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     ThaYamamoto (09-21-2020)

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    Quote Originally Posted by Norfern-Ostrobothnian View Post
    I can merge them if he wants them merged
    Wow thanks appreciate that, I'm just waiting for him to message back.

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    Turns out that the files can already be found merged in the link TheYamamoto posted.
    Processed data (1) E-MTAB-8450.processed.1.zip

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     ThaYamamoto (09-22-2020)

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