User: ali.al-fatlawi

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3 months, 1 week ago
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11 months ago
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a*************@tu-dresden.de

Posts by ali.al-fatlawi

<prev • 5 results • page 1 of 1 • next >
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Comment: C: plink association: FDR is one for all
... Thanks for your reply. Just to add one point, i have RNA. So we are having less variants (for expressed genes). So this may cause that problem. Your answer explain the issue partially, many thanks ...
written 3 months ago by ali.al-fatlawi10
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Comment: C: plink association: FDR is one for all
... Thanks for your reply. The problem is that i have significant pvalue using logistics regression model or chi-square, around 1e-5. but when adjust and calculate FDR, it is one. I believe that it shouldn’t be different that much. If there is nothing significant why logistics regression pvalue sugg ...
written 3 months ago by ali.al-fatlawi10
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plink association: FDR is one for all
... Dear Biostars, I need your help please, I am new to genome wide association studies, and now i am struggling with this issue: I have around 150 samples, of RNA sequences. I clean the data and called variants ... based on GATK workflow. Then, kept the variants with max 3% missingness in the samples ...
fdr gwas plink rna-seq written 3 months ago by ali.al-fatlawi10 • updated 3 months ago by ATpoint36k
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the absent genes in GWAS
... in GWAS for bacteria, how we can asses the SNPs that are located within a gene region if that gene is absent in some samples? do we exclude these samples from our association study? or we assume these loci as a reference? Could you please advise me. ...
genome gene sequence snp written 11 months ago by ali.al-fatlawi10
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Comment: C: PL field in gvcf file equal to zero
... Hi Pierre, as there is no called GT at this loci, in only some of the samples, could that means absence of a gene in those samples? Regards ...
written 11 months ago by ali.al-fatlawi10

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