Could you please do us another tutorial for structure with SNP because it's not clear how you used the first input file, the only thing that we see is 0, -9, and ID but without clear identification.
Hi i have done everything but i got the problem after the data phased ,because i have 15 diploid marker and 32 columns but always shw error in 32 columns can you help me out for this
qreat tutorial, thanks a lot! I have a problem when I set parameters 50k/100k, the program use just 2GB of memory out of 60GB and it takes forever to compute. How do I set a numer of nuclei and memory? Do I need to use STRUCTURE without front end?
Hi, I do not know how to change the memory assignment in Structure, or if this is possible. For larger data sets or SNP sets, the ADMIXURE program is more suitable. But this runs only on Linux or MacOS dalexander.github.io/admixture/
Thank you very much for the effort you are doing. I have benefited from your videos a lot. At minute 5:32, how was this data generated? Can you make a video in this regard? I tried to create data from Adaptmap, but I was not able to do that. Please help in this regard.
This particular data was generated via the --keep option in PLINK, but entire breeds could be selected with the --keep-fam option. More details in the video: How to select and remove individuals in PLINK th-cam.com/video/iSATTMb3pZw/w-d-xo.html
Hi, Do you mean an admixture analysis that is done without leaving the R environment? I do not have such a tutorial right now, but it is a good idea to follow up on it. So probably in the future.
Thank you Prof for this illustrative video. My question is if we run structure for more than one k ( for example k= 1-5) what are the appropriate ways (or software, R packages) can we use to chose the best k?
Hi, I will cover this in one of the future videos, where we will check out Structure Harvester. What you need to do is upload the results in a zip file there taylor0.biology.ucla.edu/structureHarvester/
Could you please do us another tutorial for structure with SNP because it's not clear how you used the first input file, the only thing that we see is 0, -9, and ID but without clear identification.
How to arrange input for multiallelic data?
Hi i have done everything but i got the problem after the data phased ,because i have 15 diploid marker and 32 columns but always shw error in 32 columns can you help me out for this
Lovely tutorials. Keep going Dr. 👍. Thank you for your efforts. These videos are priceless and very helpful for teaching my class.
What's wrong with the structure line coming out horizontally?
As always, the best tutorial ever. Thank you so much. Very comprehensive and we'll explained. This is what we call applied genetics.
qreat tutorial, thanks a lot! I have a problem when I set parameters 50k/100k, the program use just 2GB of memory out of 60GB and it takes forever to compute. How do I set a numer of nuclei and memory? Do I need to use STRUCTURE without front end?
Hi, I do not know how to change the memory assignment in Structure, or if this is possible. For larger data sets or SNP sets, the ADMIXURE program is more suitable.
But this runs only on Linux or MacOS
dalexander.github.io/admixture/
Thank you very much for the effort you are doing. I have benefited from your videos a lot.
At minute 5:32, how was this data generated? Can you make a video in this regard? I tried to create data from Adaptmap, but I was not able to do that. Please help in this regard.
This particular data was generated via the --keep option in PLINK, but entire breeds could be selected with the --keep-fam option.
More details in the video: How to select and remove individuals in PLINK
th-cam.com/video/iSATTMb3pZw/w-d-xo.html
Thank you
Thanks prof; do you have a tutor about how we can run the whole admixture/structure analysis in R than switching back to the STRUCTURE package?
Hi,
Do you mean an admixture analysis that is done without leaving the R environment? I do not have such a tutorial right now, but it is a good idea to follow up on it. So probably in the future.
Thank you Prof for this illustrative video. My question is if we run structure for more than one k ( for example k= 1-5) what are the appropriate ways (or software, R packages) can we use to chose the best k?
Hi,
I will cover this in one of the future videos, where we will check out Structure Harvester. What you need to do is upload the results in a zip file there
taylor0.biology.ucla.edu/structureHarvester/
As usual great work Professor.
Thank you so much for awesome explanation. Good job!!!!