User: seta

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seta1.1k
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Posts by seta

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Comment: C: DE analysis with edgeR and possibly batch effect
... Thank you very much for all the comments. Devon, your mean is using something like `lrt <- glmLRT(fit, coef=2)`, yes? ...
written 3 days ago by seta1.1k
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DE analysis with edgeR and possibly batch effect
... Hi all, I'm using edgeR for recognizing differentially expressed genes between control and treatment groups of mice. Here, vd_s is control and vd_r is treatment at 1 day (vd_s1 and vd_r1) and 7 days (vd_s7 and vd_r7) after birth with two replicates. I used the following code with edgeR: count ...
de analysis edger batch effect written 3 days ago by seta1.1k • updated 3 days ago by Devon Ryan88k
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Plotting Fst or zFst value
... Hi all, I was wondering if converting the Fst value to z-score (zFst) is necessary for plotting the Fst value of SNPs as the Manhattan plot? there is the Manhattan plot with both Fst and zFst in the papers. Could you please let me know your suggestion and why? Thanks ...
z-score fst manhattan plot written 24 days ago by seta1.1k
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How to get derived allele count for a list of SNPs
... Hi all, I was wondering how I can obtain the derived allele count for a list of SNP variants in human (hg 38)? I also have the corresponding vcf file for these variants. Also, please kindly let me know if I can use Fisher's test for comparing DAF (derived allele frequency) between populations? In t ...
vcf population derived allele written 4 weeks ago by seta1.1k
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Comment: C: Replace ID column of vcf file with another column in the text file
... Thank you for all your responses. At the moment, I don't access to our cluster and can't paste the error from vcf-validator. But, I think the RamRS's solution works as I have the ID column in the text file and want to replace it with the existing one. I try it. ...
written 4 weeks ago by seta1.1k
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Replace ID column of vcf file with another column in the text file
... Hi all, I have the standard vcf file (VCFv4.2) and would like to replace the ID column of vcf file with the column in the other text file. The text file (without header) is like below: 1 56782 1:56782:T:C I used the below codes to edit the vcf file: grep -P '^#' file.vcf > new.vcf ...
vcf id column edit manipulation written 5 weeks ago by seta1.1k
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How vcftools calculate Fst value?
... Hi all, I used vcftools for calculation the Fst value between two populations (pop1 and pop2) using the below command: ./vcftools --vcf file.vcf --weir-fst-pop population_1.txt --weir-fst-pop population_2.txt --out pop1_vs_pop2 However, some Fst value sounds strange to me. For example, pleas ...
populations fst vcftools written 6 weeks ago by seta1.1k
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Comment: C: Quality control on 1000 genome vcf file
... Many thanks for your nice explanation ...
written 6 weeks ago by seta1.1k
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Quality control on 1000 genome vcf file
... Hi everybody, I was wondering if (and which) quality control steps should be done on 1000 genome vcf files in the case of using them along with our population-specific vcf files? please kindly let me know your QC steps on this vcf files? Thanks ...
vcf quality control 1000 genome written 6 weeks ago by seta1.1k • updated 6 weeks ago by Kevin Blighe39k
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Comment: C: bcftools doesn't normalize the vcf file
... Currently, I have no access to the cluster, I try your example and back to you. ...
written 6 weeks ago by seta1.1k

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