User: mary

gravatar for mary
mary200
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200
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Location:
Bologna university
Last seen:
2 days, 10 hours ago
Joined:
6 years, 7 months ago
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m*********@yahoo.com

PhD  in animal breeding and genetic

Posts by mary

<prev • 51 results • page 1 of 6 • next >
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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 10 days ago by mary200
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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 10 days ago by mary200
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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 11 days ago by mary200
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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 11 days ago by mary200
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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 16 days ago by mary200 • updated 11 days ago by Kevin Blighe35k
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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 3 months ago by mary200 • updated 3 months ago by zx87546.2k
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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 5 months ago by mary200 • updated 5 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 6 months ago by mary200
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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 6 months ago by mary200
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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 6 months ago by mary200

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