User: Tao

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Tao120
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Posts by Tao

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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 3 months ago by Tao120
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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 3 months ago by Tao120 • updated 3 months ago by Philipp Bayer4.6k
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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 4 months ago by Tao120
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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 7 months ago by Tao120 • updated 7 months ago by cdsouthan1.7k
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Answer: A: How to access VCF files for Genotype Tissue Expression (GTEx) data
... Hi, You might want to be authorized first to access GTEx genotyping data. From the link below, https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000424.v6.p1, there is instructions for requestors. Once you are authorized, you can access via the Authorized Access. The genotyp ...
written 7 months ago by Tao120
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Answer: A: Filtering Imputation output: how to filter on a VCF INFO field
... Hi, This post is very helpful for me as I am also looking for protocols for QC imputation results. Besides the QC steps you mentioned above, I wonder if you add other QC steps? If yes, please kindly tell me. Thanks! Tao ...
written 9 months ago by Tao120
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Comment: C: Filtering Imputation output: how to filter on a VCF INFO field
... The extract.py seems like a script to extract the download urls. You can ignore that line and take what else you need. ...
written 9 months ago by Tao120
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Genetic Map file format: how to understand the combined_rate column and the genetic_map column ?
... Hi guys, The genotype imputation need human genetic map file, whose format is like(in chr1): position COMBINED_rate(cM/Mb) Genetic_Map(cM) 55550 0 0 568322 0 0 568527 0 0 721290 2.685807669 0.410292036939447 723819 2.8222713027 0.417429561063975 723891 2.9813105581 0.41 ...
genetic map centimorgan written 10 months ago by Tao120 • updated 9 months ago by archimyed30
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Answer: A: paste columns into one line in command line
... If your input format is like ">SAMD11_148398_chr1_879534_879961 GGTTGC", then use the following command: awk '{print $1"\n"$2}' input_file > output_file But if your input is like "SAMD11 148398 chr1 879534 879961 GGTTGC" and you want to convert it to two lines: >SAMD11_148398_chr ...
written 10 months ago by Tao120
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Imputation on two genotyping datasets: should I do imputation separately? or merge the two datasets first?
... Hi guys, I'm doing eQTL analysis. The genotyping data are from two sequencing centers using same type of SNPs chip. But one center genotyping has a better SNPs call rate than the other one: ~100,000 more SNPs were called. I did QC on two datasets separately. QC would also cause some SNPs variance ...
snps imputation eqtl genotyping written 10 months ago by Tao120

Latest awards to Tao

Popular Question 3 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 10 months ago, created a question with more than 1,000 views. For How to efficiently remove a list of reads from BAM file?
Supporter 14 months ago, voted at least 25 times.
Scholar 16 months ago, created an answer that has been accepted. For A: How to choose NCBI viral database?

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