User: Negin

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Negin0
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Posts by Negin

<prev • 43 results • page 1 of 5 • next >
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Characteristic of E. Coli - phylogroup A
... Hi, I was wondering what the main characteristics of E. Coli phylogroup A are? Can they be dangerous? I would appreciate it if someone could help me or introduce good sources regarding that to me, please. ...
bacteria e. coli phylogroups escherichia coli written 14 days ago by Negin0
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Comment: C: Why kinship is a random effect while population structure is a fixed effect in G
... I have the same question. ...
written 25 days ago by Negin0
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Comment: C: Can we conduct a QTL analysis on a haploid organism?
... I mean if we do not have the offsprings of the generation, how can we know about the outcome of recombination? ...
written 8 weeks ago by Negin0
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Comment: C: Can we conduct a QTL analysis on a haploid organism?
... thanks for your answer. And for diploid, should we have data from different generations or should we simulate the recombination? ...
written 8 weeks ago by Negin0
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Can we conduct a QTL analysis on a haploid organism?
... Hi, I am not familiar with QTL analysis, but I read little bit about it and I wondered if we can conduct a QTL analysis on a haploid organism? ...
qtl quantitative trait locus written 8 weeks ago by Negin0
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Comment: C: Batch effect in GWAS
... Dear @Kevin Blighe Actually, as I mentioned before, for the first dataset, I added 5 dimensions for controlling population structure, and for the second one, I added three. And the number of dimensions is decided based on the knee of scree plots for components of the MDS. And for the merge one, base ...
written 12 weeks ago by Negin0
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Comment: C: Batch effect in GWAS
... I applied MDS on a distance matrix for all samples based on phylogeny. ...
written 12 weeks ago by Negin0
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Batch effect in GWAS
... I am working on bacterial GWAS. I have two batches: When I applied GWAS on the first batch, I found 5 effective principal components (based on a scree plot for eigenvalues of an MDS) to control population stratification. When I applied GWAS on the second batch, I found 3 effective principal componen ...
gwas batch-effect genomics sequencing written 12 weeks ago by Negin0
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Comment: C: Problem with normalization by bcftools
... Because I can't post a long reply, I show only the variant that was part of the input, but it disappeared from the output. I hope this is helpful. Otherwise, which kind of information do you need? ...
written 3 months ago by Negin0
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Answer: A: Problem with normalization by bcftools
... Here, the example: Chromosome 2339162 . C T,A 89906.62 PASS AC=25,1; AF=0.114,4.566e-03;AN=219;BaseQRankSum=-3.610e-01;DP=17877;FS=1.706;MLEAC=25,1;M ...
written 3 months ago by Negin0

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