User: zhangdezhi008

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Posts by zhangdezhi008

<prev • 12 results • page 1 of 2 • next >
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Fst and Divergence Time
... Dear all, I resequenced 3 bird species of the same genera, species A, B and C, there was recent gene flow between A and B. The mean Fst between A and B was 0.05, and 0.6 between A and C or B and C. So, I predict that species A and B were very recently diverged compared to species C. Then I used ...
genome next-gen snp written 6 days ago by zhangdezhi0080
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Comment: C: BWA mem and BWA aln lead to different results
... Thanks for your reply very much! According to the previous study, this species should have population structure with two lineages based on sanger sequences, which is consistent with the result generated from BWA-aln. But as you said, BWA-mem should be the better solution for mapping. Confused still. ...
written 21 days ago by zhangdezhi0080
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BWA mem and BWA aln lead to different results
... Hi, all, I tried two uncover the genetic structure for a bird population using resequencing data, with PAIRED-END 100 bp reads. I used two different mapping methods BWA mem and BWA aln, and then used SAMtools to get vcf file. After filtering, we get two different SNP datasets when using BWA mem and ...
software error genome next-gen snp written 22 days ago by zhangdezhi0080 • updated 22 days ago by dariober8.2k
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How to extract W chromosome sequences from short reads data
... Dear all, I am trying to extract W-linked fragments from a re-sequenced avian individual, which has paired-end shord reads data.I have no clue about how to do this, any suggestions will help a lot! Thanks all, best regards! Dezhi ...
genome gene next-gen sequencing assembly written 6 weeks 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
... 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 6 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 6 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 6 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 6 months ago by zhangdezhi0080 • updated 6 months ago by Santosh Anand3.0k
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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 7 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 7 months ago by zhangdezhi0080 • updated 7 months ago by b.nota3.6k

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