User: User000
User000 • 250
- Reputation:
- 250
- Status:
- Trusted
- Location:
- Last seen:
- 1 week, 3 days ago
- Joined:
- 4 years, 4 months ago
- Email:
- o********@gmail.com
about me
Posts by User000
<prev
• 182 results •
page 1 of 19 •
next >
0
votes
0
answers
98
views
0
answers
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
User000 • 250
0
votes
0
answers
98
views
0
answers
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
User000 • 250
0
votes
0
answers
98
views
0
answers
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
User000 • 250
0
votes
0
answers
98
views
0
answers
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
User000 • 250
2
votes
0
answers
98
views
0
answers
... 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 ...
written 14 days ago by
User000 • 250
0
votes
0
answers
90
views
0
answers
... 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
User000 • 250
0
votes
0
answers
90
views
0
answers
... 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
User000 • 250
2
votes
0
answers
90
views
0
answers
... 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 ...
written 17 days ago by
User000 • 250
0
votes
3
answers
279
views
3
answers
... 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
User000 • 250
0
votes
3
answers
279
views
3
answers
... 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
User000 • 250
Latest awards to User000
Popular Question
10 weeks ago,
created a question with more than 1,000 views.
For Mapping RNA-seq against genome
Popular Question
10 weeks ago,
created a question with more than 1,000 views.
For Aligning BAC to an assembled sequence
Popular Question
10 weeks ago,
created a question with more than 1,000 views.
For Mapping RNA-seq against genome
Popular Question
3 months ago,
created a question with more than 1,000 views.
For Mapping RNA-seq against genome
Popular Question
5 months ago,
created a question with more than 1,000 views.
For Aligning BAC to an assembled sequence
Popular Question
7 months ago,
created a question with more than 1,000 views.
For Aligning BAC to an assembled sequence
Popular Question
7 months ago,
created a question with more than 1,000 views.
For BAM file interpretation and consensus creation
Popular Question
11 months ago,
created a question with more than 1,000 views.
For BAM file interpretation and consensus creation
Popular Question
14 months ago,
created a question with more than 1,000 views.
For Finding Overlapping, Non Overlapping Hits
Popular Question
14 months ago,
created a question with more than 1,000 views.
For Finding Overlapping, Non Overlapping Hits
Popular Question
14 months ago,
created a question with more than 1,000 views.
For Finding Overlapping, Non Overlapping Hits
Popular Question
15 months ago,
created a question with more than 1,000 views.
For Finding Overlapping, Non Overlapping Hits
Popular Question
24 months ago,
created a question with more than 1,000 views.
For Plant Annotation Workflow
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For Mapping Illumina reads against one single gene
Centurion
2.2 years ago,
created 100 posts.
Popular Question
2.5 years ago,
created a question with more than 1,000 views.
For Blast Result: Finding Non Overlapping Hits
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For Plant Annotation Workflow
Popular Question
2.9 years ago,
created a question with more than 1,000 views.
For Blast Result: Finding Non Overlapping Hits
Popular Question
2.9 years ago,
created a question with more than 1,000 views.
For Plant Annotation Workflow
Voter
3.3 years ago,
voted more than 100 times.
Rising Star
4.1 years ago,
created 50 posts within first three months of joining.
Supporter
4.1 years ago,
voted at least 25 times.
Teacher
4.2 years ago,
created an answer with at least 3 up-votes.
For A: How To Calculate Overlap Read Lengths
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1560 users visited in the last hour