User: Tao

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Tao180
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Posts by Tao

<prev • 59 results • page 1 of 6 • next >
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Comment: C: WGCNA signed vs unsigned network
... For co-expression network, I would prefer unsigned weight. But you can try both, to find out which result looks more meaningful. ...
written 10 weeks ago by Tao180
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Answer: A: WGCNA signed vs unsigned network
... I think the "sign" represents the sign of weight on the edges. If you care about the sign, for example sign represents positive or negative regulation between two nodes, then you need to choose "signed". On the other hand, if the weight just represent the strength of relatedness between two nodes, y ...
written 10 weeks ago by Tao180
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Comment: C: Filtering Imputation output: how to filter on a VCF INFO field
... That is for detecting non-biallelic variants. For example, one SNP might has 3 alleles: A -> C, A -> G. And the this step will report such SNPs as mis-match SNPs. ...
written 11 weeks ago by Tao180
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Answer: A: What exactly is sequencing depth in RNAseq?
... I want to give you a very intuitive but maybe not very accurate explanation: You can imagine each base (A/G/C/T) is a grain of rice. Suppose you sequenced a big of rice (say 100M bases), and then fill them into a very narrow but very long rice box with width = 1 grain of rice. The rice height in th ...
written 3 months ago by Tao180
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Comment: C: Does it make sense to perform Genotype Imputation using variants called from WES
... Thanks so much for your suggestions and reference! That's very helpful! This dataset is one of several datasets I used in my project, which need genotypes on whole genome, not only gene nearby regions. Luckily, we just find the genotype data call from WGS is now available for that dataset. So, that' ...
written 3 months ago by Tao180
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Comment: C: Does it make sense to perform Genotype Imputation using variants called from WES
... Hi Kevin, Thanks! You are right. Imputation can be done without any error, but how accurate it would be?That's exactly what I concerned! Thanks for your references. Best, Tao ...
written 3 months ago by Tao180
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Comment: C: Imputation on two genotyping datasets: should I do imputation separately? or mer
... For this question, in case someone would have similar situation, I'd like to answer by myself. In GTEx (v6p) protocol, they use two different genotyping array: OMNI 5M for pilot phase and OMNI 2.5M for Mid-phase. They first downsized the 5M to 2.5 M portion of variants, and then did QC and imputatio ...
written 3 months ago by Tao180
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Comment: C: Does it make sense to perform Genotype Imputation using variants called from WES
... Hi Kevin, Thanks for your reply and time! It's a public dataset, we just want to use it to fit our project which need genotype on whole genome. For the first and second reference, it seems they only imputed variants on Exome based on a reference panel of Exome sequencing project(NHLBI). For the thi ...
written 3 months ago by Tao180
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Does it make sense to perform Genotype Imputation using variants called from WES?
... Hi Biostars: I have genotype data called from Whole Exon Sequencing, which contains 0.12 million variants (most are SNPs). In theory, it is feasible to impute all SNPs on whole genome using genotype imputation model. But I am wondering how accurate it would be to use such a small portion of variant ...
whole exon sequencing genotype imputation variants written 3 months ago by Tao180
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Comment: A: In GWAS Studies, how to understand "97 SNPs explain 2.7% of BMI"?
... The rationale here is "heritability" which measures the proportion of the total phenotypic variation that's due to genetic variance. The percentage here is to describe the percentage of BMI variance due to genetic variance in the study cohort. (Total phenotypic variance = genetic variance + environ ...
written 9 months ago by Tao180

Latest awards to Tao

Popular Question 8 weeks ago, created a question with more than 1,000 views. For Extract data using awk/sed and output to different files
Scholar 10 weeks ago, created an answer that has been accepted. For A: How to choose NCBI viral database?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: WGCNA signed vs unsigned network
Popular Question 5 months ago, created a question with more than 1,000 views. For Extract data using awk/sed and output to different files
Popular Question 9 months ago, created a question with more than 1,000 views. For How to efficiently remove a list of reads from BAM file?
Popular Question 15 months ago, created a question with more than 1,000 views. For How to efficiently remove a list of reads from BAM file?
Supporter 19 months ago, voted at least 25 times.
Scholar 21 months ago, created an answer that has been accepted. For A: How to choose NCBI viral database?

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