User: nayeona.hi

gravatar for nayeona.hi
nayeona.hi50
Reputation:
50
Status:
Trusted
Location:
Last seen:
3 weeks, 4 days ago
Joined:
6 months ago
Email:
n*********@gmail.com

Posts by nayeona.hi

<prev • 16 results • page 1 of 2 • next >
1
vote
1
answer
118
views
1
answer
how to change the strand?
... Hello, I am preparing imputation for Affy 5.0 array data (Plink files). These are annotation files from Affymatrx and I have to correct all strand to 'forward', as you know. I know I should make an RS ID list files but I'm not sure what information I should keep. I will use PLINK with --flip opt ...
dbsnp imputation snp strand written 28 days ago by nayeona.hi50 • updated 27 days ago by Kevin Blighe66k
0
votes
0
answers
100
views
0
answers
about STRAND correction for imputation
... I am doing imputation with AffyMetrx 5.0 array chip data. It was quality-controlled, and I am trying (Shapeit2 and Minimac/impute2) and (Michigan Imputation Server), but keep failing. (Ref. panel: 1000 genome EAS or ASIAN) I did qc - rs Id - chr and position correction. The analysis results sa ...
flip imputation snp strand mismatch written 4 weeks ago by nayeona.hi50
0
votes
0
answers
136
views
0
answers
Comment: C: plink case/control association analysis and Manhattan plot
... you mean I have to edit the PED file (or bim file instead?) with coding 'affection column', right? Thank you and I will try. ...
written 6 weeks ago by nayeona.hi50
1
vote
0
answers
136
views
0
answers
plink case/control association analysis and Manhattan plot
... There is no one to ask about the analysis process, please advise to me. I'd like to do perform association test between case and control group. First of all, I made 'phenotype.txt' coded as 0, 1. As I'm not sure, I did 3 kind of association works for all samples, case samples, and control sampl ...
association plink snp written 6 weeks ago by nayeona.hi50
0
votes
1
answer
155
views
1
answers
Comment: C: is it possible to know individual genotype(alleles) by SNP in plink?
... `--list` and `--snp` options also worked. Thank you ...
written 6 weeks ago by nayeona.hi50
4
votes
1
answer
155
views
1
answer
is it possible to know individual genotype(alleles) by SNP in plink?
... I made 3 binary files from MAP and PED files. I'd like to know how to get individual genotypes per specific SNP. When I open the .bim file, I just see the SNP and allele information but individual information (i.e. sample Id) How to map the information? I'd like to get information like this, ...
plink snp individual written 7 weeks ago by nayeona.hi50 • updated 6 weeks ago by zx87549.7k
2
votes
1
answer
136
views
1
answer
how to make individual list file when extracting on plink?
... I made individual list file like this: N2002620115 N2002774440 N2002570297 N2002487409 N2002348348 And used commands --bfile data --keep ind_list.txt --make-bed --out According to plink web site tutorial, it must have paired columns - Family ID and Individual ID. I made ...
plink written 7 weeks ago by nayeona.hi50 • updated 7 weeks ago by zx87549.7k
0
votes
1
answer
261
views
1
answers
Comment: C: How to convert bfiles(bim/bed/fam) to PED and MAP file back?
... Thanks. Solved the errors. ...
written 10 weeks ago by nayeona.hi50
1
vote
1
answer
261
views
1
answer
How to convert bfiles(bim/bed/fam) to PED and MAP file back?
... I converted PED and MAP files to bfiles using make-bed option to change the SNP identifiers, and want to convert them to PED file back. How could I do this? ...
plink format convert written 10 weeks ago by nayeona.hi50
0
votes
0
answers
161
views
0
answers
How to analyze SNPs as variables?
... Hi, this may be the silly question, and please understand. I'd like to know the SNPs related to personalities influencing on a specific disease. such as: rs3814424 (conscientiousness) rs57590327 (extraversion) rs2164273 (extraversion) rs6481128 (extraversion) (https://www.snpedia.com/index.php/P ...
model snp written 11 weeks ago by nayeona.hi50

Latest awards to nayeona.hi

Supporter 4 weeks ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 821 users visited in the last hour