Prof. I just want to appreciate these videos. You take one from zero or a bachelor's degree knowledge of genetics to another level. Through these videos, I can now easily read scientific papers and/or books. I am still watching more of the videos on this channel, and indeed, they are helpful. MY QUESTION THEN IS DO YOU HAVE A WEBSITE AND/OR OTHER CLASSES WHERE YOU DELVE DEEP INTO THESE GWAS AND GENOMICS STUDIES?
Hi, Thank you for your kind words. There is no other website from at the moment, with additional materials for most of the stuff. Longer time ago I put together some text on the basics of use of genomic data, but nothing since. The link for this is here: genomicsbootcamp.github.io/book/
Thank you so much, professor. I really love watching your videos. In my result. the Q-Q plot is deviating in the middle. I thought this deviation has something to do with the normality of the data, but it turns out they are the SNPs of importance. Thank you very much.
@@MrWoof-ki3uo Depends on the definition of "early", could be also a lot of SNPs in the signals. But most of the time as you say, it is an indication of false positves. But if there is a consistent deviation for all SNPs, that is most likely due to population structure
Thank you for the useful videos on this channel Prof. I would like to know if correcting for population structure alone in the GWAS model is sufficient as I often hear about correcting for kinship also.
Hi, Correcting for kinship (or other words the genomic relationships) is one of the ways of population structure correction. So these two are the same.
Hello professor, Thank you so much for your useful videos, they are getting me through my MRes in Genetics! I have a question I performed an Fst analysis using your methods via Plink in R, and also have the Manhatten plot. How do I know which 'windows' were used- and what are these 'windows'? My supervisor asked about them but I was unsure. Thank you!
Hi, With the term "window" I just refer to the part of the genome around a SNP, that is important somehow. For example: Let's say there is a high Fst SNP on chromosome 1 at 15.25Mb. If you decide to look up the region in the range of 0.5Mb from this SNP, you identify the region 14.75Mb to 15.75Mb. In othe words, a 1Mb wide "window" centered on the SNP of interest.
Hi, RIght now, there are no such plans. In second half of the year there might be a bit deeper dive into GWAS, so it might come up there. But at this point I can't promise it.
Thanks for the suggestion! This is something I want to do in a "relatively" near future, but there are a few more things to clear before that. It will come, but can not tell when.
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In an era of Genotype the Phenotype is the King! Blessings 🎉
The entire playlist is Priceless. Thanks so much for the enlightenment on GWAS!
Agree, this helps enormous to understand the articles i want.
Prof. I just want to appreciate these videos. You take one from zero or a bachelor's degree knowledge of genetics to another level. Through these videos, I can now easily read scientific papers and/or books. I am still watching more of the videos on this channel, and indeed, they are helpful. MY QUESTION THEN IS DO YOU HAVE A WEBSITE AND/OR OTHER CLASSES WHERE YOU DELVE DEEP INTO THESE GWAS AND GENOMICS STUDIES?
Hi,
Thank you for your kind words.
There is no other website from at the moment, with additional materials for most of the stuff. Longer time ago I put together some text on the basics of use of genomic data, but nothing since. The link for this is here: genomicsbootcamp.github.io/book/
You are doing a great job. Priceless and mindblowing helpful. Thank you, man.
very clear introduction into GWAS! thank you
Glad it was helpful!
Thank you so much for useful information
As a master student doing a research internship about GWAS I want to thank you so much for your helpful videos 🥺❤️
It is very interesting Professor, looking forward to learn more about GWAS
Thank you so much for sharing these such valuable information!!!
Glad it was helpful!
dear professor thank you, great explanation and easy to understand
You are welcome!
Thanks for your inspiring lecture, and it really helps me to have a general idea about GWAS
Glad to hear that
Thanks so much. Are you going to have a set of video about the machine learning in genomics? That would be super of interest.
Thank you so much, professor. I really love watching your videos. In my result. the Q-Q plot is deviating in the middle. I thought this deviation has something to do with the normality of the data, but it turns out they are the SNPs of importance. Thank you very much.
In the middle already? That must be an interesting case!
Good luck with the research!
Whats your lambda value?
@@GenomicsBootCamp Doesnt lifting up early on the qq plot typically indicate inflation - so false positives
@@MrWoof-ki3uo Depends on the definition of "early", could be also a lot of SNPs in the signals. But most of the time as you say, it is an indication of false positves. But if there is a consistent deviation for all SNPs, that is most likely due to population structure
Thank you for the useful videos on this channel Prof. I would like to know if correcting for population structure alone in the GWAS model is sufficient as I often hear about correcting for kinship also.
Hi,
Correcting for kinship (or other words the genomic relationships) is one of the ways of population structure correction. So these two are the same.
@@GenomicsBootCamp Thank you for the clarification Prof. I appreciate your response a lot.
Hello professor,
Thank you so much for your useful videos, they are getting me through my MRes in Genetics!
I have a question
I performed an Fst analysis using your methods via Plink in R, and also have the Manhatten plot.
How do I know which 'windows' were used- and what are these 'windows'? My supervisor asked about them but I was unsure. Thank you!
Hi, With the term "window" I just refer to the part of the genome around a SNP, that is important somehow.
For example: Let's say there is a high Fst SNP on chromosome 1 at 15.25Mb. If you decide to look up the region in the range of 0.5Mb from this SNP, you identify the region 14.75Mb to 15.75Mb. In othe words, a 1Mb wide "window" centered on the SNP of interest.
Dear professor,
Thank you very much for your helpful videos. Would you have a plan to talk about polygenic scores derived from GWAS?
Hi,
RIght now, there are no such plans. In second half of the year there might be a bit deeper dive into GWAS, so it might come up there. But at this point I can't promise it.
Thank you so much Professor it was very interesting presentation on GWAS. Sir, I want to know step wise descriptions on work flow of performing GWAS.
Thanks for the suggestion! This is something I want to do in a "relatively" near future, but there are a few more things to clear before that. It will come, but can not tell when.
😑 P"R"O"M"O"S"M!!!