User: bha

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bha60
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Posts by bha

<prev • 47 results • page 1 of 5 • next >
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integrated analysis of SNPs and Methylation data?
... I wonder is there any good source where i can get any gidance to do "integrated analysis of SNPs and Methylation data"? I googled but can't find any usefull stuff. ...
epigenetics next-gen snp written 6 weeks ago by bha60
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Sample size calculation for GWAS?
... I want to calculate sample size to achieve certain amount of power for GWAS? We are not using any case/control, it is a discrete data. Would you please recommend which software can do this job? or any paper? ...
genome R genetics snp gwas written 12 weeks ago by bha60
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Comment: C: Phenotype from plink fam file in gcta
... Many thanks Kevin, but basic point was that if phenotype is already in test.fam, then what is point to have separate --pheno test.phen. Anyways thanks for responding ...
written 24 months ago by bha60
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Phenotype from plink fam file in gcta
... My question is about specifying phenotype file in GCTA analysis. My phenotype data is in my .fam file(sixth column). But software notes says i should make another test.phen. is it possible that GCTA read phenotype from .fam file? # MLMA analysis - If you have already computed the GRM gcta6 ...
snp gcta written 24 months ago by bha60 • updated 24 months ago by Kevin Blighe66k
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Comment: C: How to convert bgen data files to PLINK format
... I tried this: plink2 --bgen data.chr22.bgen --make-bed --out ex22 But got this error message: Error: .bgen file does not contain sample IDs, and no .sample file was specified. what am i missing in command? ...
written 2.1 years ago by bha60
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How to convert bgen data files to PLINK format
... I have sequence data which is in [.bgen format][1] . Wanted to convert this into PLINK format. Any suggestion what's the best way to do this? [1]: http://www.well.ox.ac.uk/~gav/bgen_format/ ...
software bgen plink written 2.1 years ago by bha60 • updated 24 months ago by Biostar ♦♦ 20
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How to Ranking SNPs
... I have SNPs data sets in PLINK format. I wanted to choose top 1000 only (based on p-value or some other order). I wonder, can i do this in PLINK? Or any other programme can do this SNP ranking? Any suggestion please? ...
R plink snp written 2.4 years ago by bha60
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check relatedness of individuals
... I used 1000 g data sets to simulate the sequence. After performing simulation, I got 10K individuals, for some other analyses. I wonder, how i can check the relatedness of simulated individuals with original data (individuals)? Should I first calculate simple correlation of MAF from two data sets or ...
R next-gen genetics plink snp written 2.4 years ago by bha60 • updated 2.4 years ago by Biostar ♦♦ 20
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Comment: C: How to convert Haplotypes file to PLINK format data
... yes, i think it works well. ...
written 2.5 years ago by bha60
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Comment: C: How to convert Haplotypes file to PLINK format data
... Seems like that GTOOL can do this conversion: http://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#formats ...
written 2.5 years ago by bha60

Latest awards to bha

Great Question 24 months ago, created a question with more than 5,000 views. For How do I remove duplicated by position SNPs using PLink?
Epic Question 24 months ago, created a question with more than 10,000 views. For How do I remove duplicated by position SNPs using PLink?
Popular Question 24 months ago, created a question with more than 1,000 views. For How to convert bgen data files to PLINK format
Popular Question 24 months ago, created a question with more than 1,000 views. For How do I remove duplicated by position SNPs using PLink?
Popular Question 24 months ago, created a question with more than 1,000 views. For How to convert plink.raw to map and ped files in any software
Popular Question 24 months ago, created a question with more than 1,000 views. For How to get Haplotype file from PLINK format data
Popular Question 24 months ago, created a question with more than 1,000 views. For How to convert Haplotypes file to PLINK format data
Popular Question 24 months ago, created a question with more than 1,000 views. For How to combine txt file to convert in Plink format
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How to convert plink.raw to map and ped files in any software
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How do I remove duplicated by position SNPs using PLink?

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