User: zhangdezhi008

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Posts by zhangdezhi008

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Comment: C: How can I get the proportion of variantion for PC1 and PC2 for PCA in GCTA
... Santosh, Thank you very much! Are there any methods to remedy? Actually, I have also used multidimentional scaling (MDS) for the same dataset, MDS is similar to PCA. I used the following parameters for MDS: plink --bfile plink --read-genome ibs1.genome --out mds1 --cluster --mds-plot 4. Then I got 4 ...
written 4 months ago by zhangdezhi0080
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Comment: C: How can I get the proportion of variantion for PC1 and PC2 for PCA in GCTA
... Does "SUM_TOTAL_EIGENVECS" mean to sum all eigenvalues (sum=36 in my data)? Then the first two PCs only represented 7% and 5% variation, is it too low to use? ...
written 4 months ago by zhangdezhi0080
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Comment: C: How can I get the proportion of variantion for PC1 and PC2 for PCA in GCTA
... Thanks for your reply, Santosh. But how do I know the proportion of the variation for PC1 and PC2? I have got a pca result using the parameters gcta --grm plink_grm --pca 3 --out plink_pca. The following is the eigenvalues: 2.66081 1.9079 1.62115 1.4276 1.32104 1.30427 1.17457 1.114 1.11038 1.09591 ...
written 4 months ago by zhangdezhi0080
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How can I get the proportion of variantion for PC1 and PC2 for PCA in GCTA
... Hi, all I used GCTA to do principle conponent analysis of my vcf file. And I got two files "pca.eigenval" and "pca.eigenvec", how can I get the proportion of variantion for PC1 and PC2? Any suggestions will help alot! Thanks for your attention very much! Dez ...
next-gen sequence snp written 4 months ago by zhangdezhi0080 • updated 4 months ago by Santosh Anand2.9k
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Comment: C: How to interpret genotypes with DP=1 for a vcf file
... Thanks for your reply. I will not trust the lower DP SNPs. How can one read possesses an alternative base? I also have another question, how can we know the depth for each allele for a heterozygous site? ...
written 5 months ago by zhangdezhi0080
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How to interpret genotypes with DP=1 for a vcf file
... Dear all, I used samtools for SNPs calling and vcftools for SNPs filtering. I got a vcf file with a lot SNPs.How to interpret the genotypes when DP=1? In my opinion, DP=1 means that this site has only one read, it could be homozygous 0/0 or 1/1, but how can it be a heterozygous 0/1? The following i ...
next-gen snp sequencing written 5 months ago by zhangdezhi0080 • updated 5 months ago by b.nota3.5k
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Comment: C: How to delete two populations pseudo snps from a mutiple populations vcf file?
... Hi Pierre, If using mutlple populations to call SNPs, but only paired comparison are needed, there may have some sites are not SNPs anymore. And also, using multiple populations would omit biallelic SNPs only exist in the focal two populations, because these kind SNPs may become triallelic or tetra ...
written 8 months ago by zhangdezhi0080
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How to delete two populations pseudo snps from a mutiple populations vcf file?
... Hi all, I used three populations to call snps by SAMtools.And filtered biallelic snps by vcftools, I need to calculate between populations's fst, the original vcf file was divided into 3 sub-vcf files, each sub-vcf only contains two populations. The variant sites exist in the original vcf for t ...
genome snp sequencing written 8 months ago by zhangdezhi0080 • updated 6 months ago by Biostar ♦♦ 20

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