User: Tao

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Tao140
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Posts by Tao

<prev • 56 results • page 1 of 6 • next >
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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 15 days ago by Tao140
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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 17 days ago by Tao140
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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 20 days ago by Tao140
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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 20 days ago by Tao140
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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 20 days ago by Tao140
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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 21 days ago by Tao140
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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 6 months ago by Tao140
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In GWAS Studies, how to understand "97 SNPs explain 2.7% of BMI"?
... Hi guys, I'm a newbee on GWAS study and I saw sentences in a talk by John Quackenbush that "97 SNPs explain 2.7% of BMI" "All common SNPs may explain 20% of BMI" What's the meaning of that percentage? How are the percentages calculated? Thanks! Tao ...
gwas written 6 months ago by Tao140 • updated 6 months ago by Philipp Bayer4.8k
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Comment: C: How to remove a list of reads from fastq file?
... import fileinput import sys import os reads_to_remove_path = sys.argv[1] fp = open(reads_to_remove_path) remove_list = [] while True: line = fp.readline() line = line.strip() if not line: break remove_list.append(line) ...
written 6 months ago by Tao140
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How to get gene full description with Ensembl IDs?
... Hi, I have a list of genes with ensembl ID from both gencode_v14 and gencode_v19 GTF files. I want to get the full descriptions of them, here, the full description is like: "Leucine-rich repeat-containing protein 37A2" whose Ensembl ID is ENSG00000238083.3. It would be perfect to have downloaded p ...
gene annotation ensemble written 9 months ago by Tao140 • updated 9 months ago by cdsouthan1.8k

Latest awards to Tao

Popular Question 10 weeks ago, created a question with more than 1,000 views. For Extract data using awk/sed and output to different files
Popular Question 6 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 12 months ago, created a question with more than 1,000 views. For How to efficiently remove a list of reads from BAM file?
Supporter 16 months ago, voted at least 25 times.
Scholar 18 months ago, created an answer that has been accepted. For A: How to choose NCBI viral database?

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