User: mary

gravatar for mary
mary210
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210
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Bologna university
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3 weeks, 5 days ago
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7 years, 3 months ago
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PhD  in animal breeding and genetic

Posts by mary

<prev • 52 results • page 1 of 6 • next >
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How can I count the number of time the SNP appearance on ROH?
... Hi all Sorry if it is a basic question I am studying on ROH in some European sheep breed. Runs of homozygosity were defined for individuals in each of populations using PLINK v1.9. To identify the genomic regions that were most commonly associated with ROH (ROH Islands), the percentage of the occu ...
roh snp written 27 days ago by mary210 • updated 27 days ago by zx87548.2k
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Comment: C: why my ROH file result does not include some chromosome
... yeah, I did as below 1- tail -n +2 mapv2.txt > scottisheep.map 2- tail -n +2 ped.txt > 6firstcol_scot 3- tail -n +2 genotypes.txt > genotype_pedfile 4- perl -ne '($id, $tmp) = split( / /, $_, 2 ); $tmp =~ s/ //g; print "$id "; print join(" ", split( //, $tmp ) );' scott752_1.ped > ...
written 8 months ago by mary210
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Comment: C: why my ROH file result does not include some chromosome
... nothing to be filtered because I did quality control before that . the data is free. you can download from https://datadryad.org/resource/doi:10.5061/dryad.8f191. after downloading, I make ped and map file and use for my research. I worry about may be I make some mistake when contract ped and map f ...
written 8 months ago by mary210
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Comment: C: why my ROH file result does not include some chromosome
... **Hi . I check statistics for chr12 for sample and I check log and data. no noticeable thing was found; see my log file below:** Options in effect: --file scott_corrected2 --chr 12 --noweb --out rest12 --missing 38884 (of 38884) markers to be included from [ scott_corrected2.map ] ...
written 8 months ago by mary210
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Comment: C: why my ROH file result does not include some chromosome
... Hi Kevin I have 15 sheep breeds, when I check number of SNP in most of them, they are same and I have ROH in all studied breed, unless this breed that I ask question. so I dont think it was main problem. I download my data from https://www.datadryad.org/. may be the data had problem? ...
written 8 months ago by mary210
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why my ROH file result does not include some chromosome
... Hi, I am using plink to calculate runs of homozygosity. For 50k ovine data. After Quality control I use folow comand: plink --file mydata --homozyg-snp 40 --homozyg-density 100 --homozyg-kb 1000 --sheep --out mydata_roh I got Plink.result.hom, it just have ROH for fist 11 chromosome. I che ...
snp plink runs of homozygosity. 50k ovine written 8 months ago by mary210 • updated 8 months ago by Kevin Blighe48k
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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 11 months ago by mary210 • updated 11 months ago by zx87548.2k
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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 14 months ago by mary210 • updated 13 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 14 months ago by mary210
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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 14 months ago by mary210

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Great Question 8 months ago, created a question with more than 5,000 views. For How Can I Do Principal Components Analysis ?
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