More posts like this
-
Any recommendation for calculating Fu and Li's D using RStudio?
written by Chatchapon •I'm currently working on a project that requires me to calculate Fu and Li's D using RStudio. Previously I would use the package PopGenome. However, …
-
PopGenome stats for each population
written by Yixuan •Hi, I am using PopGenome to compare statistics such as Fst, nucleotide diversity, and Tajima's D among populations. My VCF file contains information on individuals …
-
Fst Values calculated by 2 different methods were slightly different. Why?
written by kopelol •Hi, I tried to calculate Fst Values per SNPs using Popgenome(R package) and vcftools, but the value calculated by each methods were slightly different. Do …
-
Calculating pi and phi from VCF files on R
written by maho4822 •Hello all, I'm trying to calculate the pi and phi values for 3 different VCF files. I have attempted to download the packages VCFtools, DNAsp, …
-
the function of readVCF in PopGenome R package
written by mike229lin •Hello I'm using PopGenome R package to calculate Fst with vcf files. I met some problems during the protocol First, I want to analyze whole …
-
Population genetic inference from pooled-DNA microsatellite genotyping
written by apaspati •Hello, I have a dataset from genotyping pooled dna, which has the informacion of the allele frequencies for the microsatellite loci in each populations e.g. …
-
PopGenome fasta input
written by tiffany.kosch •Hello All- I would like to use PopGenome to analyze sequence diversity by individual and population. My sequences are currently in fasta format. I was …
-
Extract several fields from vcf file
written by kelly.wang135Hello all, I'd like to modify my vcfs to contain several info only. There are "GT:AD:DP:FT:GQ:PL:PP" in format column, but I want to include "GT,DP,GQ" …
-
Calculating FST from Transcriptomic Sequence Data stored in a VCF
written by mek362 •Hi all, I am working with *de novo* - assembled transcriptomes, and would like to estimate a suite of neutrality and F stats for each …
-
It's there an R package to map QTL and work with F1 population?
written by tobal.92 •Hi. I'm trying to find if there's an R package to work with a F1 population and get QTLs. I know about the existance of …