User: mary

gravatar for mary
mary190
Reputation:
190
Status:
Trusted
Location:
Bologna university
Last seen:
1 month, 2 weeks ago
Joined:
6 years, 3 months ago
Email:
m*********@yahoo.com

PhD  in animal breeding and genetic

Posts by mary

<prev • 45 results • page 1 of 5 • next >
0
votes
0
answers
127
views
0
answers
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 8 weeks ago by mary190 • updated 6 weeks ago by Biostar ♦♦ 20
0
votes
0
answers
153
views
0
answers
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 9 weeks ago by mary190
0
votes
0
answers
153
views
0
answers
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 9 weeks ago by mary190
0
votes
0
answers
153
views
0
answers
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 9 weeks ago by mary190
0
votes
5
answers
217
views
5
answers
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 9 weeks ago by mary190
0
votes
5
answers
217
views
5
answers
Comment: A: a problem with read ped file in plink?
... thanks a lot every body, all of them worked ...
written 9 weeks ago by mary190
0
votes
5
answers
217
views
5
answers
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 9 weeks ago by mary190
0
votes
5
answers
217
views
5
answers
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 10 weeks ago by mary190
7
votes
5
answers
217
views
5
answers
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 10 weeks ago by mary190 • updated 9 weeks ago by zx87545.0k
1
vote
0
answers
4.5k
views
0
answers
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 4.0 years ago by mary190

Latest awards to mary

Great Question 4.0 years ago, created a question with more than 5,000 views. For How Can I Do Principal Components Analysis ?
Great Question 4.0 years ago, created a question with more than 5,000 views. For Remove Some Snps In Plink
Great Question 4.0 years ago, created a question with more than 5,000 views. For Make Ped And Map File For Plink Anlysis
Epic Question 4.0 years ago, created a question with more than 10,000 views. For Make Ped And Map File For Plink Anlysis
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Make A Special File By Plink
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Haplotype Reconstruction
Popular Question 4.0 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 4.0 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 4.0 years ago, created a question with more than 1,000 views. For How To Reconstruct Haplotypes And Visualize Them In Haploview
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 Linkage Disequilibrium Analysis
Popular Question 4.0 years ago, created a question with more than 1,000 views. For how can I recode phased haplotype?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Remove Some Snps In Plink
Popular Question 4.0 years ago, created a question with more than 1,000 views. For How Can I Make Sweeps Input File?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Ld Analysis
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Problems Installing Fastphase
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Make Ped And Map File For Plink Anlysis
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Recombination Result By Phase
Commentator 4.0 years ago, created a comment with at least 3 up-votes. For C: Haplotype Construction Using Phase Version 2.1
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 Problems Installing Fastphase
Scholar 4.2 years ago, created an answer that has been accepted. For A: Remove Some Snps In Plink
Popular Question 6.3 years ago, created a question with more than 1,000 views. For Make Ped And Map File For Plink Anlysis

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 633 users visited in the last hour