User: Tao
Tao • 120
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Posts by Tao
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0
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... 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
Tao • 120
1
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1
answer
190
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1
answer
... 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
...
written 3 months ago by
Tao • 120
• updated
3 months ago by
Philipp Bayer ♦ 4.6k
0
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3
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3
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... 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
Tao • 120
8
votes
2
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... 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 ...
0
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1
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1
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... 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
Tao • 120
0
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3
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... 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
Tao • 120
0
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3
answers
1.9k
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3
answers
... 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
Tao • 120
5
votes
1
answer
462
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1
answer
... 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 ...
1
vote
2
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352
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... 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
Tao • 120
0
votes
0
answers
420
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0
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... 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 ...
written 10 months ago by
Tao • 120
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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?
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16 months ago,
created an answer that has been accepted.
For A: How to choose NCBI viral database?
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