User: User000

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User000250
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Posts by User000

<prev • 182 results • page 1 of 19 • next >
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Comment: C: DAPC different clustering results
... So, if I run max.n.clust = 20, how can I get the membership values then for K 2-20? ...
written 13 days ago by User000250
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Comment: C: DAPC different clustering results
... yes, but I want to get the consistent results, similar to admixture, like from K = 2 to K = 20 I want to see consistent results of species separating at the end in 20 different clusters...I hope I could explain myself. ...
written 14 days ago by User000250
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Comment: C: DAPC different clustering results
... update: for n.clust = 20 I did set.seed(20), and it worked 3 times, for n.clust = 19, should I use also set.seed(20)? ...
written 14 days ago by User000250
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Comment: C: DAPC different clustering results
... No, I have two different versions, and I am interested in one of them, the problem is I want consistent results for all runs from K 2 to K 20. I already know that I want to stop at K 20, and not go further. So I literally have to re-run the same command line 50 times? Isn't n.start = 1000 doing thi ...
written 14 days ago by User000250
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DAPC different clustering results
... Dear all, I am using find.clusters and DAPC to my SNPs data. I am interested in K 2-20. However, the clustering results are different whenever I re-run the code on the same dataset, I guess this is due to k-means algorithm that find.clusters is using. Do you know it if possible to find an optimum ...
R k-means dapc find.clusters written 14 days ago by User000250
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Comment: C: Performing fast bootstrap in R using ape package
... I am running it also on a cluster with 10 cores (I don't know exactly how many cores I am allowed to use) and is still running also 3 days. Without bootstrap it takes me around 1-2 hours. Thank you a lot for the advice, I am now running it,let's see ...
written 17 days ago by User000250
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Comment: C: Performing fast bootstrap in R using ape package
... yeah, it says Running parallel bootstraps... and also is using 6 cores... Do you think it is enough for 5000 snps and something is going wrong? ...
written 17 days ago by User000250
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Performing fast bootstrap in R using ape package
... Dear all, I would like to perform a nj tree with 1000 bootstrap on my snp data. I have around 5K snps and I am using R package ape: snp <- as.matrix(objt) stree = nj(dist.gene(snp)) myBoots <- boot.phylo(stree, snp, function(xx) nj(dist.gene(xx)), B = 1000, mc.cores = 6) It ha ...
R bootstrap ape written 17 days ago by User000250
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Comment: C: Variant calling for a polyploid species
... I did state the programs I am using. It is not so difficult to find the best practice etc, however I think it is not so straightforward when dealing with the polyploid species. So I wanted to know if there are some particular parameters to use or filtering etc. Thank you anyway ...
written 3 months ago by User000250
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Comment: C: Variant calling for a polyploid species
... Hi Nicolas thank you! I already did all of these steps. But I have very specific questions I stated above. ...
written 3 months ago by User000250

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