User: Javier2013

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Javier201390
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Posts by Javier2013

<prev • 8 results • page 1 of 1 • next >
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Software Programs For Estimating Effective Population Size (Ne) Using Genome-Wide Snp Data
... Hi everyone: I wanted to know If any of you had any experience using any software program that can give effective population size estimates based on genome-wide SNP data. Thank you. Javier ...
population snp written 5.6 years ago by Javier201390 • updated 5.5 years ago by jackuser1979860
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Answer: A: How Does Ld In Plink Work?
... Hi: If anyone is interested I finally got a logical result. My problem was that my genetic map was not accurate; thus my LD was completely wrong. The parameters I used in plink were these: --r2 --ld-window-r2 0 --r2 --ld-window 99999 --ld-window-kb 70 Then I just this script to plot the result ...
written 5.6 years ago by Javier201390
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Comment: C: How Does Ld In Plink Work?
... Hi Clare, I just tried rerunning the test without that option but the results are pretty much the same! I do not understand why. I makes no sense given the fact that it is an African population. I do not know what else to do. ...
written 5.6 years ago by Javier201390
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Programs For Estimating Admixture Dates Using Genome-Wide Snp Data?
... Hi: This is a general question. I wanted to what software programs are currently available for estimating admixture dates using genome-wide SNP data? I was using ALDER and ROLLOFF, but since I want to date an admixture event from a close related population to my test population I do not get any ...
snp written 5.6 years ago by Javier201390 • updated 12 weeks ago by Biostar ♦♦ 20
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Using Snp Weights To Test For Admixture Dates Using Alder
... Hi everyone: I am using the software ALDER to estimate admixture dates using genome-wide data (SNPs). I have seen that in most articles instead of using the allele frequency differentiation between the ancestral populations, the weights for each SNP is used to run the program. Does anyone know h ...
gwas snps written 5.6 years ago by Javier201390
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Answer: A: Genotype For Latino Population
... If you want to use genotype data to examine your Latino population the best way to do that is to use either a Dimentionality reduction technique such as PCA or MDS or a Clustering Algorithm such as that implemented by ADMIXTURE or STRUCTURE. I guess the paper you're referring to was using some of ...
written 5.6 years ago by Javier201390
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Answer: A: Convert Admixture Q Outputs Into Dendograms
... Hi Tonig: If you want to create a phylogenetic tree using your GWAS data I would highly recommend you to use a standard genetic distance for the distance matrix and not just an euclidian distance. For example, you could calculate Fst values (between your populations or individuals) and then use thi ...
written 5.6 years ago by Javier201390
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Answer: A: Admixture Dating
... Hi Tim: Yes, it is possible to estimate admixture dates using only one surrogate population, although this is only implemented in ALDER and not in ROLLOFF. The main idea is this (from Dienekes Blogspot): This is a useful application of the idea that you don't need both reference populations to es ...
written 5.6 years ago by Javier201390

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