Відео

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

Hi sir, I need to merge 22 plink binary files into one sir, kindly advice Thanks in advance

Man I don't know who are you, but you are awesome! Thanks for your lectures

This channel is an excellent source to learn and teach. Thank you so much

Professor Gabor, I hope you will continue with the topic of selection signature in the near future. Thank you for your instructive videos

At 3:40 you talk about a critical mass. Can you define that in terms of subscribers and views?

Good idea. Msc trees and divergence time estimates are what is on my plate nowadays.

Do you have ay web site ?

I really appreciate your channel and offer my suggestions. Your notion of dealing with broader population genomics topics thru SNP analysis is excellent and I think draws in a broader audience, especially if you help with workflows that provides phasing data, kinship, and population structure that is beyond plink. I personally am interested in canine data and am working toward breed analysis. The struggle is the data wrangling required to use data from diverse research. For example getting data into phasing software like Beagle continues to frustrate me. Broader topics about moving around in SNP files for example would be welcomed by me. Why and how do you phase SNP data, and when is imputation necessary. Broader topics like this would not pull in the “general” audience but should interest more people than plink-specific programs.

I have a question: if we have a CG heterozygous (like I do have in my data), how will the scan differentiate both green signals and not misinterpret it as being homozygous? The illumina reference guide itself does now cite "fluorophore", not even once. And both there and in their videos, they only show biotin associated with C and G, which after will have a green signal, and DNP with A and T, with a red signal. How is it possible to differentiate CG or AT heterozygous?

Hello respected Sir, Please make a video on how to run XPCLR? or just show how to convert vcf file into .geno format?

Those are great! My two cents: Ctrl + I to indent rows Ctrl 1 and Ctrl 2 to switch between Console and Script Ctrl + L to clear the console Ctrl + Shift + N for a new Script

can you have such video in which you calculate the region of selected regions in selective sweep analysis? i am unable to do

Dear Professor, this is very helpful. thank you. I have two questions? 1. what if I want to update the phenotype column with an outcome coded as 0 and 1 (No, Yes), wouldn't the zeros be considered missing? 2. what happens if the number of individuals in the phenotype file is not proportional to that in the genotype files?

i have to read so many papers for my molecular biology degree and struggle with really understanding them. this was really helpful, thank you so much for sharing!!

A video on how to annotate the manhattan plot will be very useful🙏🙏