Thank you for the tutorial. Just wonder after identifying 3 (in this example) fitted with the dataset. But there were 3 runs for K=3, How do we select the run?
The Structure is similar to Admixture, related to the questions it answers. So in this regard, I think they are interchangeable. With this said, Admixture might also come at some point. GWAS will surely come, but no dates on this yet.
The Structure harvester webtool is broken. Therefore, could you please have anyone share me the any you link for python 3 for structure harvester to determine and visualize best K value?
Hi, I do not know about any papers to cite on this, but my "rule of the thumb" approach was always go for about 10% of the follow up analysis. So if that is 100k, I would go for a 10K burn in, in addition to that.
Hi - it looks like the structure harvester link doesn't work anymore ? Do you know if there are any alternatives ? Thank you - and thank you for your tutorials :)
Hi, the link seems to be broken. I added the GitHub page with the latest version there, but likely has a different means to run as the one shown in the video.
I am very glad you are making these videos despite having a very limited number of viewers.
Thanks!
Thank you so much for the video, it's very useful for me. Before watching, I had to calculate delta K by excel and it took lot of time.
It is very helpful tutorial and am highly satisfied! Thanks and Keep it up!
Thank you for making this video! (I'm in Germany too)
Thank you for the tutorial. Just wonder after identifying 3 (in this example) fitted with the dataset. But there were 3 runs for K=3, How do we select the run?
Thank you! Very informative!
Thank you!!
Will be more helpful if you provide tutorial on Admixture analyses using admix tool for GWAS or other tool.
The Structure is similar to Admixture, related to the questions it answers. So in this regard, I think they are interchangeable. With this said, Admixture might also come at some point.
GWAS will surely come, but no dates on this yet.
my Evanno method could not work. can I infer the number of subpopulation only from the L(K) graph?? Thanks in advance
The Structure harvester webtool is broken. Therefore, could you please have anyone share me the any you link for python 3 for structure harvester to determine and visualize best K value?
How to determine the recommended burnin and mcmc? 50000? 200000? 300000? How to choose?
Hi,
I do not know about any papers to cite on this, but my "rule of the thumb" approach was always go for about 10% of the follow up analysis. So if that is 100k, I would go for a 10K burn in, in addition to that.
Hi - it looks like the structure harvester link doesn't work anymore ? Do you know if there are any alternatives ?
Thank you - and thank you for your tutorials :)
Hi, the link seems to be broken. I added the GitHub page with the latest version there, but likely has a different means to run as the one shown in the video.
@@GenomicsBootCamp Thank you so much ! Strangely enough, the original link is now working again!
@@kai9908 Please can you assist with the link that works perfectly? mine is still not accessible. thank you
@@mohammedkingimi3415 Hey there ! Sorry but I didn't actually do anything to fix it, the link randomly started working after waiting for 1 day !