Great tutorial... I have learned how to convert HAPMAP format into Vcf format file from your tutorials. But, can you please clarify me how to get population text/ grouping details.? or is the Population text are gropuping result of Population structure analysis?
Very nice video. Now that the QC work is completed and we have cleaned data in various formats, such as.vcf, could you please show us how to use it for GWAS analysis with the rMVP package?
A very detailed and helpful video! About the parameter you chose for --indep-pairwise command, is there any good tutorials or guidelines for that? For example, how to choose the window size (50 in the video)? How to choose the threshold for r^2 (0.2 in the video)?
Thanks a lot for your nice video
Great tutorial... I have learned how to convert HAPMAP format into Vcf format file from your tutorials. But, can you please clarify me how to get population text/ grouping details.?
or is the Population text are gropuping result of Population structure analysis?
Grouping information was not from structure software. For teaching purposes, individuals were randomly divided into groups.
Very nice video. Now that the QC work is completed and we have cleaned data in various formats, such as.vcf, could you please show us how to use it for GWAS analysis with the rMVP package?
Here is the link: ruclips.net/video/cp3yIARAyEI/видео.htmlsi=YXtdF7q2jiZeX23N
A very detailed and helpful video! About the parameter you chose for --indep-pairwise command, is there any good tutorials or guidelines for that? For example, how to choose the window size (50 in the video)? How to choose the threshold for r^2 (0.2 in the video)?
Thank you very much, appreciate it.
Is the vcf file a merged from individual vcf files of 36 genotypes or is it concatenated one?
It's concatenated.
Thanks a lot
No problem
Amazing tutorial. Can you please explain how to prepare pop file.
Thank you.
Nice video! What data set was used for the demonstration? Is it open access?
its open access, you may download it from snp-seek.irri.org/_download.zul
where I found the Rscript you are using ?
github.com/mohsinali1990/My_scripts
Please teach us how you made the input vcf file.
Please check this link: www.internationalgenome.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-40/
where can we get this R script plzz reply sir
github.com/mohsinali1990/My_scripts
sir what is this "pop.txt" ?
github.com/mohsinali1990/My_scripts
how can we get population grouping info
is it possible to get the R script you use for the analysis
github.com/mohsinali1990/My_scripts
Hello, Can I get your rice36indi.vcf file please?
Sure, I will share a dropbox link later.
@@MohsinAli-xn4cl can you share please
Nice video. What is the pop.txt file?
hi are u studying genomics ?
github.com/mohsinali1990/My_scripts/blob/main/pop.txt
Sir please make vedio on how we can go for analysis in GAPIT 3
+1