User: Victor

gravatar for Victor
Victor10
Reputation:
10
Status:
New User
Location:
Australia
Last seen:
7 months, 3 weeks ago
Joined:
2 years, 11 months ago
Email:
w*******@uni.sydney.edu.au

Posts by Victor

<prev • 6 results • page 1 of 1 • next >
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how to plot the genotype of every SNP
... Hi, According to the post of Kevin Blighe, https://www.biostars.org/p/379208/#379295 I am wondering how to plot the genotype of every SNP for a single sample. Are there any R-packages can be used? ...
R allele genotype snp plot written 8 months ago by Victor10 • updated 8 months ago by AsoInfo300
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how to deal with 0 in allele from ped/map files
... Hello, I have a ped/map files generated from illumina final report by perl script. Then I found out that I have many "-" in the allele1 or allele2. I check the perl script and the script will make "-" into "0". Anyway, I am doing the position selection and I dont need the 0 in my plink file (raw ...
plink ped map written 2.0 years ago by Victor10
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The same loci for XP-EHH by Selscan
... Hello, I try to use selscan to compute the value of xpehh by selscan. But when I try to run it. I got the error message about the two dataset need have same loci? I am not sure what is the same mean and how to make the same loci from two populations for XPEHH process by SELSCAN? I feed the vcf fil ...
xpehh selscan plink written 2.1 years ago by Victor10
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How to generate the map file for selscan?
... Hello I have 2 datasets and want to analysis the XPEHH scores by selscan. I used plink and beagle to pre-process my datasets. When I try to run the selscan. my datasets have same haplotypes but not the same loci in my map file? I dont understand why my map file can not work in selscan. Do you hav ...
selscan phase plink beagle written 2.3 years ago by Victor10
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the XP-EHH instruction
... Hello, I am trying to get the XP-EHH values by using HP-EXX. (https://github.com/joepickrell/xpehh) . I only have map and ped plink files in two populations. So 1. I used plink function --recode vcf, to make vcf files (preQC had been done, plus --snp-only -just acgt). 2. Eeagle was applied to phase ...
vcf xp-ehh haplotype plink phased written 2.3 years ago by Victor10 • updated 4 months ago by shanshuwen900
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How to convert PLINK file (map, ped) to haplotype file for XPEHH application
... Hello I am the first year PhD student in University . Basically, I'm new to PLINK (obviously). Sorry for asking quite a silly question. I am doing the selection signal with canine and try to use the HP-EXX (https://github.com/joepickrell/xpehh) to get the haplotype score. However, I only have ...
genome snp written 2.4 years ago by Victor10 • updated 2.4 years ago by Wietje210

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