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What does the --cow parameter do? I cannot fin it in the documentation.

Sadly, the R script has been recently taken down from the pastebin website :( Great video tho!

Wait until that person finds out that ancestry informative genes don't necessarily affect phenotype.

How to determine the recommended burnin and mcmc? 50000? 200000? 300000? How to choose?

Thomas Michael White Michael Allen Thomas

Anderson Gary Hernandez Daniel White Michael

Allen Christopher Williams Linda Williams Anthony

Wilson Mary Harris Daniel Anderson William

Sir, you are a great man who spreads knowledge beyond the border. Thanks One thing we need to learn is not available on social platforms, and it is XP-CLR. Do you have any idea about it or tutorials? Please share with us. Especially its files generation process

Do you know how to fix this issue "Warning: 199 het. haploid genotypes present (see C:/Users/User/GWAS/HapMap/Data/CEU/QC_1/QC_11.hh )"

share the scripts in a manageable form

there is no scripts here

very interesting... it seems to me that genetics is like microeconomics and genomics is like macroeconomics in economic terms. thank you.

Very nice video! Would you mind helping on this error? : I keep getting the error: finalReport_tidy %>% distinct('Sample ID') %>% mutate(FID = "Sheep", sire = 0, dam = 0, sex = 0, phenotype = -9) %>% relocate('Sample ID', .after = FID) %>% write_delim("final_report.fam", col_names = F) Error in `relocate()`: ! Can't select columns that don't exist. :heavy_multiplication_x: Column `tSample ID` doesn't exist. For some reason my columns are shown like this: colnames(finalReport_tidy) [1] "SNP Name\tSample ID\tAllele1 - Forward\tAllele2 - Forward\tAllele1 - Top\tAllele2 - Top\tAllele1 - AB\tAllele2 - AB\tGC Score\tX\tY" Do you maybe know what is wrong? I am trying to analyze a sheep genome

Thank you for the tutorial, great content as always! Do you see any particular advantage from using SLEMM instead of doing the GWAS in PLINK?

Hello! Will this series help me to set up a base for studying genomics for masters level at Wageningen University and Research?

Thank you so much. Is it possible to merge the Affymetrix-based plink file with illumina genotypes?

Sir, you the G!!! 👏👏

thank you so much❤！ Wise and great sense of humor

Just a minor note. From the perspective of the offspring; when recombination occurs during meiosis in one of the parents, it are the grandparents chromosomes that recombine.

Thank you, this really helped.

Thank you

Thank you for a video. Please, could you explain the difference btw. LD pruning and LD clumping? (a part of a procedure for the calculation of polygenic risk score).

This is fun

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

The number represent each group on the map in which it determined the group equilibrium (intelligence). Africans has the highest!!

Thank you so much for making us understand complex concepts in simple way!

"But wait, there is more" 🤣. Thanku for sharing these information!

How to import data set to the R software?

sorry where and how to import the database

Well explained. Yet I am unable to understand it completely but it's good to learn new things 😊

Beautifully explained with clarity. Thank you so much for helping me.

Thank you for these wonderful videos! I did the goat PCA in the previous video, and did the same PCA (so all goats, not the filtered breeds) using this video's strategy as well, just to compare apples to apples (or goats to goats). The plots look the same, though mirrored across the x axis, but the % in the X and Y axis labels between the two PCAs are very different. Could you explain why the %s are different for PC1 and PC2 for the entire goat population when looking at a plot made using the previous video's method of "doing the math in R" vs. this one's "doing the math with PLINK"? I posted this question Monday, but I think it didn't go through because I'd included a URL, a link to a github with my showing what I'm talking about. So I'll break this up so it's not a clickable link: github(dotcom)/kln-rdn/goatquestion

Womp womp

Please, can you explain how to install GEMMA? Thnaks

We need a web site also for easy access

Thank you for the channel and for sharing your expertise in genomics with the others. I would like to ask a question, I am not familiar with the programming at all and I need to analyze polygenic risk scores in my patients (I have whole exome sequencing data and also a selected GWAS I would like to extract SNPs from), I understand (to a certain extent) the principle of the calculation, but I do not know how to write the program. Would you please recommend to me, what should I do - to learn programming and do it on my own or to order it as a service (where?). I am doing research on a complex disease and I am collecting data longitudinally, so I would need the calculations repeatedly. I would be happy to receive any advice. Thank you.

is that possible to use TAssel for hCMV gen polymorphism analysis ?

I use chatgtp similarly. English is not my first language, so as a free grammar corrector is very helpful

Thank you. That is very helpful. Please add a link to your scripts .

When i go to website and download the data then it appears 4 kinds of files. which file do i need to put in the system while doing quality control? (1file:map, 2nd file: ped, 3rd: marker_id INFO, 4th: selection)

Thank you very much for your lessons! Thanks for your work! You provide a huge amount of useful information! Special thanks to you for your scripts.

I’m new here in your channel and I am very fascinated with your videos. Thank you so much!!!!!

Whether from plink we can detect ROH estimation from pooled whole genome data?

hello, I'm getting this error message Error: Failed to open plink.log. Try changing the --out parameter. I tried to change the permissions but is still occurring, I'm using Ubuntu

What's wrong with the structure line coming out horizontally?

Can this tool varLD be used to compare the LD of two diseases involving common complex traits? I'm very sorry if my question is very wage, I am new to this field.

Top-notch presentation

Thank you so much! It worked for me and rly helped a lot!

Hi sir, I need to combine the 22 vcf files to one vcf file