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Post by djoser-xyyman on Sept 12, 2018 12:05:57 GMT -5
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Post by djoser-xyyman on Sept 12, 2018 12:06:14 GMT -5
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Post by djoser-xyyman on Sept 12, 2018 12:06:27 GMT -5
Quote from the paper: “Data availability. The mapped BAM files for the 90 mitochondrial samples and three nuclear samples are deposited in the European Nucleotide Archive (http://www.ebi.ac.uk/ena) with the study ID ERP017224. JK2888 and JK2911. For JK2134
Our analysis furthermore shows that derived alleles for the genes SLC24A5, known to be responsible for partially lighter skin pigmentation were present in both JK2888 and JK2911 (see Supplementary Note 6 for details). For further genes such as SLC45A2, LCT and EDAR we were unable to find derived alleles for both JK2888 and JK2911. For JK2134, there was no sufficient coverage after quality filtering at all the specific sites, which is why the analysis revealed no further clues”
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Post by djoser-xyyman on Sept 12, 2018 12:41:04 GMT -5
Here is another illustration. Glactools converting Abusir BAMs files to TreeMIX input format or even PLINK I am surprised Dr S Keita and others haven’t delved into this?!
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Post by djoser-xyyman on Sept 13, 2018 10:48:34 GMT -5
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Post by Deleted on Sept 13, 2018 12:31:53 GMT -5
Ok! We are making progress. But it seems like they have indeed removed the CODIS STR from the 3 Abusir mummies. They have even modified many on-line analysis tools delete the STR functions and capabilities. But we are still working on it. I see why they have chosen to concentrate on Chr 21? I have done analysis so far on Chr 21. We are working on others. I'm impressed with your erudition and passion for this stuff. To paraphrase your favorite quote: "Without and opinion, you only have a mess of data". So what's your opinion on the 3 Abusir Mummies and how does it differ from the official one? How do the graphs and other stuff you've been posting buttress your opinion? Your data dump is wasted on me since I lack the expertise to make sense of it. I suspect that I'm not the only one. Please post your view and your argument why the data support your view on the Abusir mummies. It might be useful if you did a tutorial on the data and how it is evaluated. "But it seems like they have indeed removed the CODIS STR from the 3 Abusir mummies." Why would that be meaningful? "I see why they have chosen to concentrate on Chr 21? I have done analysis so far on Chr 21. We are working on others." I'm glad you "see it", now help the rest of us do the same. Who are the others you are working with and what do you want to determine? Thank you for clarifying these issues.
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Post by djoser-xyyman on Sept 13, 2018 15:29:26 GMT -5
Ok! Since some of you may be at a loss on what this thread is about
Here goes ….. Some(3) of the Abusir mummies autosomal data set has been released and freely available to download. But the researchers have NOT released the autosomal STR like they did with the Armana mummies (King Tut and his family). The CODIS STR profile shows geographic affiliation and is the standard use by forensic experts to identify “closest too”. Forensic experts do NOT use SNP frequency. Keeping in mind STR are essentially LD and transmitted as “blocks of genes”.
My assumption is although a limited and selective set of the genomic data of the Abusir was released it may be possible to pull “some” CODIS STR from the few SNPs they released. Labeling SNP as “Eurasian” and “non-African” and the like is misleading and it is deliberate because non-African and Eurasian SNPs all originated in Africa. CODIS STR will show alignment to Modern Geographic populations. I expect the Abusirs to be geographically aligned to the Great Lakes Africans just as the Armanas since they lived within 100 miles of each other.
How do we determine that? Comparing apples vs Apples.. Compare CODIS STRs of the Abusir to CODIS STRs of global modern populations just as the FBI would. Makes sense?
Since I have some “downtime” I decided to look at different software packages. I now realize IT CAN BE DONE…..if the ”correct region” of the Abusir genomes were released. Apparently BAM Analysis kit ver 1.5 , 1.4 had that capability but during the upgrade to ver 1.6 and above it was REMOVED. But there are other ways around it which we are working on.
So far I can safely say that Some software came up empty in trying to pull CODIS STR from the Abuisr!!!!! But bewilderingly that same software can pull OTHER STRs(non-CODIS) so I know the software is working which leads me to believe the CODIS STRs were removed deliberately before they rest of the dataset was made available. ElMeastro of ES suggested that to me in one thread I think he may be right! I am seeing that myself.
I have pulled many Phenotypic SNPs from the ABusir so far but it is hard to separate African from European because believe it or not Europeans and Africans are so genetically similar!! The Abusir were clearly not Asians based upon what I am getting . I posted some relevant material above so far.
I have done computer programming in the past unfortunately it is PC based like C++ etc. I am now getting into Unix and Ubuntu with my downtime. Most packges that can do the job is not windows based but Unix or Pyton etc essentially mainframe
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Post by Deleted on Sept 13, 2018 18:37:23 GMT -5
Thank you for this clear statement of what you're up to. Have you contacted the people who did the analysis of the Abusir mummies, if you did, what reasons did they give for deviating from normal procedures such as removing the CODIS STR from the 3 Abusir mummies?
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Post by zarahan on Sept 14, 2018 7:57:28 GMT -5
XYZ says: My assumption is although a limited and selective set of the genomic data of the Abusir was released it may be possible to pull “some” CODIS STR from the few SNPs they released. Labeling SNP as “Eurasian” and “non-African” and the like is misleading and it is deliberate because non-African and Eurasian SNPs all originated in Africa. CODIS STR will show alignment to Modern Geographic populations. I expect the Abusirs to be geographically aligned to the Great Lakes Africans just as the Armanas since they lived within 100 miles of each other. Indeed. Pre-labeling samples "Mediterranean", or "Eurasian" or "non-African" and excluding certain data - thus distorting the overall picture and diversity when the final analysis is published, is a common pattern with some European researchers. Keita points out the same pattern as far back as the 1920s and 1930s. He has a good recent critique of the same games being run, almost a century later..
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Post by djoser-xyyman on Sept 14, 2018 10:53:08 GMT -5
Odd that I am now pulling autosomal STRs from the Abusirs(3) but not the CODIS STRs(at least up to this point)!!!. I am doing it Chromosome by Chromosome. A slow process. It looks like they removed the CODIS STRs as ElMaestro speculated BEFORE making the genome freely available to the public. Also I am getting some SNPS but none are informative. But I will keep plugging away.
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Post by djoser-xyyman on Sept 14, 2018 10:55:59 GMT -5
Using BAM Kit(SNP) I got this for ONE chromosome for one(1) of the 3 Abusir. There is a African presence. But we are only looking at ONE Chromosome from ONE ABusir. Trying to find out what is "Mediterranean"/ But there is no definition
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Post by Tukuler al~Takruri on Sept 14, 2018 15:07:09 GMT -5
I don't know the 1st thing about it but don't you want results from filtered-autosomal-o37-results.csv.gz from the BAM Analysis Kit instead of Dienekes' dodecad admixture results? Using BAM Kit(SNP) I got this for ONE chromosome for one(1) of the 3 Abusir. There is a African presence. But we are only looking at ONE Chromosome from ONE ABusir. Trying to find out what is "Mediterranean"/ But there is no definition
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Post by chatoyer on Sept 14, 2018 22:06:03 GMT -5
Here is another illustration. Glactools converting Abusir BAMs files to TreeMIX input format or even PLINK I am surprised Dr S Keita and others haven’t delved into this?! osf.io/ecwf3/
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Post by zarahan on Sept 14, 2018 23:09:03 GMT -5
Odd that I am now pulling autosomal STRs from the Abusirs(3) but not the CODIS STRs(at least up to this point)!!!. I am doing it Chromosome by Chromosome. A slow process. It looks like they removed the CODIS STRs as ElMaestro speculated BEFORE making the genome freely available to the public. Also I am getting some SNPS but none are informative. But I will keep plugging away. Keep up the good work. Being as folk are running anayses through the various tools, Keita himself did run popAffiliator above on the Armanas and found that African presence. But what are reasons Abusir authors removed the CODIS STRs?
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Post by djoser-xyyman on Sept 16, 2018 5:35:12 GMT -5
"what are reasons Abusir authors removed the CODIS STRs?" You said it yourself. Keita used popAffl! Popaffliator=CODIS STRs. In other words to use PopAffliator the CODIS STRs must be present. They were removed from the Abusir before being uploaded(it seems) Thus you can NOT run PopAffliator on the Abusir. Thus no comparison to modern geographic populations like what we have for the Amarnas. Odd that I am now pulling autosomal STRs from the Abusirs(3) but not the CODIS STRs(at least up to this point)!!!. I am doing it Chromosome by Chromosome. A slow process. It looks like they removed the CODIS STRs as ElMaestro speculated BEFORE making the genome freely available to the public. Also I am getting some SNPS but none are informative. But I will keep plugging away. Keep up the good work. Being as folk are running anayses through the various tools, Keita himself did run popAffiliator above on the Armanas and found that African presence. But what are reasons Abusir authors removed the CODIS STRs?
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