User: evolozzy

gravatar for evolozzy
evolozzy10
Reputation:
10
Status:
New User
Location:
University of Pennsylvania
Website:
https://evolozzy.net/
Twitter:
evolozzy
Last seen:
17 hours ago
Joined:
1 year, 4 months ago
Email:
o**********@protonmail.com

Posts by evolozzy

<prev • 6 results • page 1 of 1 • next >
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Answer: A: R: poppr: Problems converting vcf to genclone object
... I've found a solution, using `pegas` with`vcfR`. This causes another problem but it is easy to come up with a workaround. While reading vcf files with `read.vcf` the positions of the SNPs might not be read, so I get that information using `getPOS` and put that into the data frame created by `pegas ...
written 17 hours ago by evolozzy10
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R: poppr: Problems converting vcf to genclone object
... I can convert VCF to genclone by reading vcf data with `vcfR`, converting to into genind and then into genclone object in two separate ways, however, each conversion results in a different problem. ---------- **Method 1** genIndObj<-vcfR2genind(vcf,ploidy=1,strata=Loc) genCloneObj< ...
R poppr genind genclone written 2 days ago by evolozzy10
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Comment: C: snpEff build Error
... Were you able to solve this problem? I've tried renaming the chromosome names in gff and fasta files to same name however, ended up having `Protein check: mtDNA OK: 0 Not found: 13 Errors: 0 Error percentage: NaN%` ...
written 16 days ago by evolozzy10
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Comment: C: Assigning separate samples to groups in a vcf file
... I converted to PLINK format, it helped, thanks! ...
written 4 months ago by evolozzy10
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Comment: C: Assigning separate samples to groups in a vcf file
... It is about conducting statistical tests on the sample groups. I have poolseq data from 3 different groups that I want to compare, and 5-6 samples in each group. I have the VCF file that contains all of my samples. ...
written 4 months ago by evolozzy10
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Assigning separate samples to groups in a vcf file
... I have some VCF files from several experiments, each containing multiple samples. I want to assign them into groups, according to the experimental setup. How can I assign each sample to a group in VCF file, or should I do it during post-processing? ...
variant calling snp written 4 months ago by evolozzy10

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