User: mary

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mary180
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Bologna university
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PhD  in animal breeding and genetic

Posts by mary

<prev • 38 results • page 1 of 4 • next >
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Comment: C: a problem with read ped file in plink?
... Hi Kevin I downloaded the data from https://datadryad.org, and yes I need to do what you wrote. I can do it on R but I want to know can I do it on bash ...
written 2 days ago by mary180
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a problem with read ped file in plink?
... Hi all I have two txt file (file1: genotype.txt and file2: 6first coloum of ped), I used them to make ped with paste file1.txt file2.txt which use it for make a ped. the problem is that when I run plink with : Options in effect: --ped scottsheep.ped --map scottisheep.map --noweb it give me t ...
plink ped written 3 days ago by mary180 • updated 3 days ago by finswimmer3.6k
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Comment: C: how can I make input file for Haploview from Output files of inferred haplotypes
... Hi Kumar Unfortunately I still have problem with making input file of Haploview. I think I have to make Legen file format, but i dont know how? ...
written 3.8 years ago by mary180
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Answer: A: how can I recode phased haplotype?
... Output files for inferred haplotypes or imputed genotypes contain two lines per given diploid individual, with the order of individuals corresponding to that supplied in the input file. In addition, summary information is given, such as a recapitulation of some of the parameters from the fastPHASE r ...
written 4.0 years ago by mary180
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what is the minimum number of indivisals and SNPs for phasing haplotype?
... Hello all as the title implies, how many individual and SNP be needed to haplotype phasing be accursed. as I understood , if I have a limited number of individuals per population and also SNP it caused phasing will be very inaccurate.I have 5 population with 400 to 1000 animal, I reconstructed hapl ...
haplotype phasing written 4.0 years ago by mary180 • updated 4.0 years ago by Biostar ♦♦ 20
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how can I recode phased haplotype?
... Dear all I have reconstructed haplotype from fastPHASE for each chromosome, as you know it has 0 /1 code, is there any way to recode it to A=1, C=2, G=3, T=4 by PLINk or any other software. any help will be appriciated ...
haplotype recode written 4.0 years ago by mary180 • updated 3.4 years ago by evo_genomics30
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how can I make input file for Haploview from Output files of inferred haplotypes by fastPHASE?
... Dear all I am doing LD analysis and selection signature on 50k snp data of cattle. For the analyses, fully phased haplotype data were required. After filtering process, I reconstructed haplotypes for every chromosome using default parameters in fastPHASE (Scheet & Stephens 2006).( Reconstructed ...
haploview phased haplotypes fastphase written 4.0 years ago by mary180 • updated 3.9 years ago by Biostar ♦♦ 20
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Comment: C: Haplotype Construction Using Phase Version 2.1
... You can use plink for recoding plink format to fastPHASE by ''--recode-fastphase'' option in PLINK. It’s similar to PHASE input file format, you should just add S for SNP and M for microsatellite marker on 4th raw as locus type ...
written 4.0 years ago by mary180
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Comment: C: Make A Special File By Plink
... Hi Matt thanks for your guide, actually I am new in haplotype phasing, I know I can use fastPHASE or PHASE for haplotype phasing (Stephens, Smith et al. 2001). I did it in Linux but i don't have enough memory for haplotype reconstruction of whole chromosome. and also when I reconstruct partial segm ...
written 4.7 years ago by mary180
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Comment: C: Make A Special File By Plink
... Hi I want to make a input file of sweep v1.1 software. Sweep accepts a standard format of genotype data, fully phased with missing data filled in. it should be two file 1. Genotype data file and 2. SNP data file. Genotype data file contain Column 1: the individual identifier. - Column 2: the ...
written 4.7 years ago by mary180

Latest awards to mary

Great Question 3.8 years ago, created a question with more than 5,000 views. For How Can I Do Principal Components Analysis ?
Great Question 3.8 years ago, created a question with more than 5,000 views. For Remove Some Snps In Plink
Great Question 3.8 years ago, created a question with more than 5,000 views. For Make Ped And Map File For Plink Anlysis
Epic Question 3.8 years ago, created a question with more than 10,000 views. For Make Ped And Map File For Plink Anlysis
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Make A Special File By Plink
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Haplotype Reconstruction
Popular Question 3.8 years ago, created a question with more than 1,000 views. For what is the minimum number of indivisals and SNPs for phasing haplotype?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Delet Some Raw In Map File And Corosponed Coloum In Ped File In Linux
Popular Question 3.8 years ago, created a question with more than 1,000 views. For How To Reconstruct Haplotypes And Visualize Them In Haploview
Popular Question 3.8 years ago, created a question with more than 1,000 views. For How Can I Do Principal Components Analysis ?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Linkage Disequilibrium Analysis
Popular Question 3.8 years ago, created a question with more than 1,000 views. For how can I recode phased haplotype?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Remove Some Snps In Plink
Popular Question 3.8 years ago, created a question with more than 1,000 views. For How Can I Make Sweeps Input File?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Ld Analysis
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Problems Installing Fastphase
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Make Ped And Map File For Plink Anlysis
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Recombination Result By Phase
Commentator 3.8 years ago, created a comment with at least 3 up-votes. For C: Haplotype Construction Using Phase Version 2.1
Popular Question 4.0 years ago, created a question with more than 1,000 views. For How Can I Do Principal Components Analysis ?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Problems Installing Fastphase
Scholar 4.0 years ago, created an answer that has been accepted. For A: Remove Some Snps In Plink
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Make Ped And Map File For Plink Anlysis

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