User: mary

gravatar for mary
mary190
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190
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Location:
Bologna university
Last seen:
1 month, 1 week ago
Joined:
6 years, 5 months ago
Email:
m*********@yahoo.com

PhD  in animal breeding and genetic

Posts by mary

<prev • 46 results • page 1 of 5 • next >
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How can I allow to hetro and missing genotype in ROH detection?
... Hi I study about ROH in some sheep breed. I want to found ROH in 1-3, 3-6, 6-12, 12-18, >18 category. for long ROH I need to correction for missing and hetro genotype. for example: I need to allow one hetrozygot and 3 missing genotype on ROH segment with more than 16 Mb lenght. dose any body ...
missing roh plink hetro written 5 weeks ago by mary190 • updated 5 weeks ago by zx87545.6k
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make ped file from SNPChip final_report
... Hi All I have a file which Here are the first 14 lines of an Illumina "Final Report" CSV file: [Header] GSGT Version 1.9.4 Processing Date 6/16/2015 3:09 PM Content SheepHD_AgResearch_Cons_15041608_A.bpm Num SNPs 606006 Total SNPs 606006 Num Sa ...
snp plink ped written 3 months ago by mary190 • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: run plink with locus has more than 2 alleles
... Hi I cheak every thing that may be related to this problem, but unfurtunatly its dosent work. the first column (sample IDs) is Familly IID in ped file so I think its not related. just may be I make wrong command in this step (python -c "import sys; print('\n'.join(' '.join(c) for c in zip(*(l.spl ...
written 3 months ago by mary190
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Comment: C: run plink with locus has more than 2 alleles
... Hi, this is 2th sample in ped file. let me I write my command for make a.ped: 1- I have this file: SNP_Name,Chr,Coordinate,R923A04,R921B12,R921C12,R921D12,R921E12 CL635944_160.1,0,0,--,CC,CC,CC,TC,TC CR_594.1,0,0,--,TT,TT,TT,TT,TT CR_816.1,0,0,--,CC,TT,TT,TT,TT 2- I use these two command & ...
written 4 months ago by mary190
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run plink with locus has more than 2 alleles
... dear All I make ped and map file on shell, when I read file by plink I get below problem; ./plink --file test --noweb --missing-genotype N 54241 (of 54241) markers to be included from [ test.map ] ERROR: Locus 1 has >2 alleles: individual R921C12 273487 has genotype [ T C ] but ...
snps plink roh written 4 months ago by mary190
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Comment: C: A problem with read ped file in plink?
... thanks alot, it work but I have plate number at the first of each raw and I wont its seperate. I means I have R921B02 GG TT AA GG ... R921E06 TT AA GG CC... I want R921B02 G G T T A A G G ... R921E06 T T A A G G C C... ...
written 4 months ago by mary190
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Comment: A: a problem with read ped file in plink?
... thanks a lot every body, all of them worked ...
written 4 months ago by mary190
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Comment: C: a problem with read ped file in plink?
... Hi , I use above command but I get this error awk: program limit exceeded: maximum number of fields size=32767 FILENAME="-" FNR=1 NR=1 I try to install and use gawk , but I use Ubuntu 12.04 I think the package I am looking for doesn't existand. so I am looking Python script to do that dose an ...
written 4 months ago by mary190
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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 4 months ago by mary190
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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 written 4 months ago by mary190 • updated 4 months ago by zx87545.6k

Latest awards to mary

Great Question 4.2 years ago, created a question with more than 5,000 views. For How Can I Do Principal Components Analysis ?
Great Question 4.2 years ago, created a question with more than 5,000 views. For Remove Some Snps In Plink
Great Question 4.2 years ago, created a question with more than 5,000 views. For Make Ped And Map File For Plink Anlysis
Epic Question 4.2 years ago, created a question with more than 10,000 views. For Make Ped And Map File For Plink Anlysis
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Make A Special File By Plink
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Haplotype Reconstruction
Popular Question 4.2 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 4.2 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 4.2 years ago, created a question with more than 1,000 views. For How To Reconstruct Haplotypes And Visualize Them In Haploview
Popular Question 4.2 years ago, created a question with more than 1,000 views. For How Can I Do Principal Components Analysis ?
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Linkage Disequilibrium Analysis
Popular Question 4.2 years ago, created a question with more than 1,000 views. For how can I recode phased haplotype?
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Remove Some Snps In Plink
Popular Question 4.2 years ago, created a question with more than 1,000 views. For How Can I Make Sweeps Input File?
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Ld Analysis
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Problems Installing Fastphase
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Make Ped And Map File For Plink Anlysis
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Recombination Result By Phase
Commentator 4.2 years ago, created a comment with at least 3 up-votes. For C: Haplotype Construction Using Phase Version 2.1
Popular Question 4.3 years ago, created a question with more than 1,000 views. For How Can I Do Principal Components Analysis ?
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Problems Installing Fastphase
Scholar 4.4 years ago, created an answer that has been accepted. For A: Remove Some Snps In Plink
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Make Ped And Map File For Plink Anlysis

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