User: mary

gravatar for mary
mary210
Reputation:
210
Status:
Trusted
Location:
Bologna university
Last seen:
7 months, 3 weeks ago
Joined:
8 years, 3 months ago
Email:
m*********@yahoo.com

PhD  in animal breeding and genetic

Posts by mary

<prev • 55 results • page 1 of 6 • next >
0
votes
0
answers
212
views
0
answers
how can I use VCF file SNP annotation?
... Hi all, I study about CNV in equus caballus. I need to make pfb file based on ecab3.0 , I looking forward to find lastest SNP annotation and find VCF file in ftp://ftp.ensembl.org/pub/release-98/variation/vcf/equus_caballus/ . I be confuse for that which file may have SNP annotation. I searched ...
vcf file snp cnv written 9 months ago by mary210
0
votes
0
answers
224
views
0
answers
Comment: C: where can I found ecab3.0 SNP annotation?
... Thanks a lot for your reply. there is three file for equus caballus here, when I extract them they have more than 65167 SNP. so I am confusing now, I have a litter familiar with VCF format so, which file in a file that I can remap with that my old map file? ...
written 9 months ago by mary210
0
votes
0
answers
224
views
0
answers
where can I found ecab3.0 SNP annotation?
... Hi every one, I appreciate if someone helps me. I am trying to make PFB file for CNV analysis in horse. So where can I find SNP annotation file of Equ Cab 3 . any suggestion will be appreciate. ...
genome ecab3.0 snp written 9 months ago by mary210
1
vote
0
answers
272
views
0
answers
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 13 months ago by mary210 • updated 13 months ago by zx87549.6k
0
votes
1
answer
698
views
1
answers
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 20 months ago by mary210
0
votes
1
answer
698
views
1
answers
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 20 months ago by mary210
0
votes
1
answer
698
views
1
answers
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 20 months ago by mary210
0
votes
1
answer
698
views
1
answers
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 20 months ago by mary210
2
votes
1
answer
698
views
1
answer
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 21 months ago by mary210 • updated 20 months ago by Kevin Blighe65k
0
votes
0
answers
452
views
0
answers
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 23 months ago by mary210 • updated 23 months ago by zx87549.6k

Latest awards to mary

Epic Question 9 months ago, created a question with more than 10,000 views. For Remove Some Snps In Plink
Popular Question 9 months ago, created a question with more than 1,000 views. For how can I recode phased haplotype?
Great Question 20 months ago, created a question with more than 5,000 views. For How Can I Do Principal Components Analysis ?
Great Question 20 months ago, created a question with more than 5,000 views. For Remove Some Snps In Plink
Great Question 6.0 years ago, created a question with more than 5,000 views. For How Can I Do Principal Components Analysis ?
Great Question 6.0 years ago, created a question with more than 5,000 views. For Remove Some Snps In Plink
Great Question 6.0 years ago, created a question with more than 5,000 views. For Make Ped And Map File For Plink Anlysis
Epic Question 6.0 years ago, created a question with more than 10,000 views. For Make Ped And Map File For Plink Anlysis
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Make A Special File By Plink
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Haplotype Reconstruction
Popular Question 6.0 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 6.0 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 6.0 years ago, created a question with more than 1,000 views. For How To Reconstruct Haplotypes And Visualize Them In Haploview
Popular Question 6.0 years ago, created a question with more than 1,000 views. For How Can I Do Principal Components Analysis ?
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Linkage Disequilibrium Analysis
Popular Question 6.0 years ago, created a question with more than 1,000 views. For how can I recode phased haplotype?
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Remove Some Snps In Plink
Popular Question 6.0 years ago, created a question with more than 1,000 views. For How Can I Make Sweeps Input File?
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Ld Analysis
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Problems Installing Fastphase
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Make Ped And Map File For Plink Anlysis
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Recombination Result By Phase
Commentator 6.0 years ago, created a comment with at least 3 up-votes. For C: Haplotype Construction Using Phase Version 2.1
Popular Question 6.2 years ago, created a question with more than 1,000 views. For How Can I Do Principal Components Analysis ?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1511 users visited in the last hour