User: gulcek

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gulcek10
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10
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New User
Location:
Turkey
Last seen:
4 years, 9 months ago
Joined:
5 years, 1 month ago
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g*********@gmail.com

Posts by gulcek

<prev • 10 results • page 1 of 1 • next >
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Answer: A: ceph/ utah pedigree 1463 members no difference in genomic data
... The columns in dbSNPannotated file is in this way: dbSnpId    alleles    chromosome    begin    end    reference    alleleAGenotype    alleleBGenotype    loci    so on.. dbsnp.132:rs112750067    C/T    chr1    10326    10327    T    NO-CALL    NO-CALL    2    no-call    no-call            I extrac ...
written 4.8 years ago by gulcek10
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ceph/ utah pedigree 1463 members no difference in genomic data
... Among (maternal) grandmother and grandfather of utah pedigree 1463, I cannot find any difference in their genomic data.  I use snp rsids, alleles, chromosome ad its beginning point to compare different members genomic data. I compare their snp allels, but only different alleles are in the chromosome ...
snp written 4.8 years ago by gulcek10
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find matching rows based on snp ids
... I have 2 files, one is about 7 MB and other is 1 GB. The first file seems: rs58108140    A/G    chr1    10582 rs10218492    A/G    chr1    10827 rs10218493    A/G    chr1    10903 and the second one is: rs58108140  rs10218493  rs11240777 I need to search second files snps in the first file and r ...
snp written 4.8 years ago by gulcek10 • updated 4.6 years ago by Biostar ♦♦ 20
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converting vcf to gds losing some snps
... I have vcf files of many individuals that I converted from 23andme raw data. I need to convert vcf files to gds files. I preprocessed the raw data so that all individuals have same rsnpids but when I convert vcf files to gds files many snps are disappearing. All individuals have same common snps  wh ...
vcf gds written 5.1 years ago by gulcek10 • updated 4.4 years ago by Biostar ♦♦ 20
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combining gds files into one gds file
... I converted 23andme raw snp data to vcf format for 750 individuals and all of them have same rsnpid's. Then I convert them to gds format using convertVcfGds(vcf, gdsfile) function in SNPRelate package. I need to merge all individual's gds files into one gds file and use it for hieararchical clusteri ...
gds snprelate written 5.1 years ago by gulcek10
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plink mergelist put many individuals into same binary file set
... We have some difficulties about using 23andMe data on plink. We have raw 23andMe snp data for each individual (total of 756). We converted each individual file to binary fileset .bed,.bim, .fam via plink. plink --23file $file --out $a After creating binary set for each individual, we converted them ...
bed merge plink written 5.1 years ago by gulcek10 • updated 4 months ago by Dawn0
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Comment: C: defining reference alleles in 23andMe file to create plink .ped file
... What is the usage of --a2-allele flag? What is input file and output file format? Could you post an example usage? I have .bim, .fam and .bed fileset of my 23andMe individuals now, how do input these to plink --a2-allele? ...
written 5.1 years ago by gulcek10
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How to obtain human genotype data from dpSNP ftp?
... I want to obtain all.vcf from dbSNP ftp to human learn reference alleles. After download human9606 all.vcf, i want to convert bed file in plink. plink --vcf All.vcf --extract snpids.txt --make-bed But it gives follwing error https://www.cog-genomics.org/plink2 (C) 2005-2015 Shaun Purcell, Christo ...
vcf dbsnp genotype plink written 5.1 years ago by gulcek10 • updated 5.0 years ago by Adam990
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defining reference alleles in 23andMe file to create plink .ped file
... I created .ped and .map pairs of each individual from 23andMe raw text format by using plink. As far as i know,  plink --bfile binary_fileset --recode 12 --out new_text_fileset --recode 12  command creates a genomic 0,1,2 matrix (If reference allele is A and genotype is AA, it gives 2, if genotype ...
snp ped plink written 5.1 years ago by gulcek10 • updated 5.1 years ago by chrchang5236.9k
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eigenstrat smartpca input files
... I want to apply eigenstrat's smartpca to 23andme raw snp datasets for 1500 people, there should be  3 input files to use smartpca : genotype file, individual file and  snp file. In individual file I need to indicate indivudal's case or control label. how do I label each individual either case or con ...
eigensoft pca eigenstrat snp written 5.1 years ago by gulcek10 • updated 5.0 years ago by rbagnall1.6k

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