User: zhangdezhi008

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Posts by zhangdezhi008

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Do I need to trim adapters and remove PE contaminators for mate-pair libraries b
... Thanks for your reply. I made a mistake, it was not adptors for MP library, it should be juctions of MP reads. So juctions should also be removed before using ALLPATHS, right? ...
written 3 months ago by zhangdezhi00810
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Do I need to trim adapters and remove PE contaminators for mate-pair libraries before using ALLPATHS
... Dear all, I am trying to use ALLPATHS-LG to denovo assemble a bird species genome (~1.1Gb). I prepared 3 libraries, including 350 bp insertion PE libary (60Gb reads), 3kb MP library (30Gb reads) and 8kb MP library (30Gb reads), all are 150 bp PE sequenced. As you can see, I did not prepared a fra ...
genome assembly next-gen written 3 months ago by zhangdezhi00810 • updated 3 months ago by h.mon26k
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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 19 months ago by zhangdezhi00810
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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 19 months ago by zhangdezhi00810
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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 19 months ago by zhangdezhi00810 • updated 19 months ago by dariober10k
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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 20 months ago by zhangdezhi00810
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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 2.1 years ago by zhangdezhi00810
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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 2.1 years ago by zhangdezhi00810
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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 2.1 years ago by zhangdezhi00810
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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 2.1 years ago by zhangdezhi00810 • updated 2.1 years ago by Santosh Anand4.8k

Latest awards to zhangdezhi008

Popular Question 3 months ago, created a question with more than 1,000 views. For How can I get the proportion of variantion for PC1 and PC2 for PCA in GCTA
Popular Question 18 months ago, created a question with more than 1,000 views. For How can I get the proportion of variantion for PC1 and PC2 for PCA in GCTA
Popular Question 18 months ago, created a question with more than 1,000 views. For How to interpret genotypes with DP=1 for a vcf file

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