User: filippo.corponi

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4 months ago
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1 year, 5 months ago
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Posts by filippo.corponi

<prev • 5 results • page 1 of 1 • next >
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PCA: summarize results from principal components analysis and look for population heterogeneity
... Hi! I am conducting a GWAS. I used plink 1.9 (--pca) to obtain first 10 population principal components which I entered in the regression model as covariates to correct for population stratification. I would like to the use the .eigenvec file, which is the output from plink --pca containing populat ...
principal components analysis pca plink written 9 months ago by filippo.corponi10 • updated 9 months ago by Kevin Blighe41k
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Comment: C: Tag SNPs - how to easily and effectively select them
... I am running it from the tagger service available online at this link: http://archive.broadinstitute.org/mpg/tagger/server.html I have not downloaded haploview and I am trying to carry out the procedure online. Once I select 'I want to upload my own genotype data as a PED file' I proceed to uploa ...
written 10 months ago by filippo.corponi10
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Comment: C: Tag SNPs - how to easily and effectively select them
... Thanks for you reply! I'm quite new to bioinformatics actually and am trying to familiarize with Haploview first. I have converted my binary (.bed, .bim, .fam) files to pedigree format (.ped, .map) via --recode in plink. I'am trying to upload the .ped file to Haploview Tagger. Any idea why I get thi ...
written 10 months ago by filippo.corponi10
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Tag SNPs - how to easily and effectively select them
... I am working with genomic data using hg19 grch37. I need to select tag SNPs for a number of genes I need to study. I've annotated my data and extracted available SNPs mapping within my gene of interest. Once I've got my list of variants I can get tag SNPs in plink using: > plink --bfile mydata - ...
genome tag snps snp gene written 10 months ago by filippo.corponi10 • updated 10 days ago by Biostar ♦♦ 20
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(Closed) vcftools - installing on MAC
... I'm trying to install vcftools on mac. Looking at previous posts on this issue, I made sure I've got Mac OS X developer tools (http://www.cnet.com/how-to/install-command-line-developer-tools-in-os-x/). I followed the procedure recommended in the official documantion (https://vcftools.github.io/examp ...
vcf vcftools written 13 months ago by filippo.corponi10 • updated 11 months ago by Biostar ♦♦ 20

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