Great, the video sounds very new again. Please, may I know the cause of missing genotypes in SNP data? Because as I know or believe, the genome does not or should not have gaps (Or is it normal for a genome to have gaps?).
No, the physcal genome itself does not have gaps, there is no "hole" in there. The missing genotypes are due to the inaccuracies in genotyping. If the accuracy of the genotyping is below a certain limit, the machine assigns it to missing, rather than take a guess. The whole process is explained in the "Illumina BeadChip genotypes - The basics" ua-cam.com/video/DHcCv6u0I3M/v-deo.html on this channel, the SNP missingness is discussed around minute 4 of that video.
Hi, I have a question , is that possible if some one with different haplogroup for example haplogroup O has same SNPs with some one else with haplogroup j1 ?
Nice lesson, thx! Btw, could you promt the PLINK function to find most probable parent for offspring given SNPs of both? (but relationship "parent-offspring" isn't identified, just SNPs and birth dates are at disposal)
Yes. You can calculate IBD with the --genome option, but this is better if you have a larger set of individuals. It computes the IBD between each pair, and the 0.5 or similar then indicates parent-offspring (or full-sib relationships). If from the birth dates it is not obvious which one it is, you have to do a paternity control using mendelian rules with --mendel, also in PLINK
@@GenomicsBootCamp yeah, forgot to mention I have around 70 individuals for search. As I got it correct, while evaluating IBD with -- genome option, should I input exactly one of the .ped and .map file formats you mentioned in the video as the -- file argument?
@@yanketzer5480 well... all individuals should be in one single ped+map file, then you put this as then input for --file and the --genome option. As a result you get a file with IBD between each pairwise combination, and you could check on the IDs you are interested in
@@GenomicsBootCamp oh, got it. Even received some result (if "0.5" value mentioned above refers to PI_HAT coefficient :). Thank you for helping me puzzle things out! +1 Subscriber :)
@@GenomicsBootCamp But unfortunately, paternity control with --mendel option doesn't work (I used it together with --genome option). Warning message pops up like "Skipping --mendel since there are no trios". I suppose family_id (or any known parentage) should be included to make it work. It's a pity that those moments are not enough documented in PLINK for such newcomers like me :(
There are plenty of open access data sets on the internet, e.g. on Dryad, but also elsewhere. I fetured some of these data sets on the channel, see videos in the playlist "Open access genomics data" ua-cam.com/play/PLdf-U83sN48Mu2x8hvmdwg5TwR6Z_GYhe.html
As far as I know their are 4 nucleotide In DNA - ATGC , what does those datasets means in which they have only 2 character like A , B or 0 , 1. How will they represent those 4 nucleotide??? What does that A and B mean. Pls help, I got confused 😕
Could please share me your references or the books for this subject? You helped a lot to understand but I need to know more about SNP for myself to understand the whole picture and to for my exam
Hi, the contents of the videos, inluding the theoretical lectures on "Introduction to Genomics" are based on my expriences and work in the field. Of course I got this knowledge from somewhere, but it was through various papers and talking to colleagues and students. It might well be that a similar book exists, but I don't know any reference to point it out.
Here are the presentations for the "Introduction to Genomics" lecture series (separate playlist on the channel. pptx-s to download: github.com/GenomicsBootCamp/IntroductionToGenomics
Wonderful video , SNP has so much in common with Hamas
Wonderful video. I learned so much. Thank you!
Great introduction to SNP data Gabor!
Thanks! I am happy you like it!
Excellent 👍
Really you are the saver
Great, the video sounds very new again. Please, may I know the cause of missing genotypes in SNP data? Because as I know or believe, the genome does not or should not have gaps (Or is it normal for a genome to have gaps?).
No, the physcal genome itself does not have gaps, there is no "hole" in there. The missing genotypes are due to the inaccuracies in genotyping. If the accuracy of the genotyping is below a certain limit, the machine assigns it to missing, rather than take a guess. The whole process is explained in the "Illumina BeadChip genotypes - The basics" ua-cam.com/video/DHcCv6u0I3M/v-deo.html on this channel, the SNP missingness is discussed around minute 4 of that video.
Thank you for the video.
Hi, I have a question , is that possible if some one with different haplogroup for example haplogroup O has same SNPs with some one else with haplogroup j1 ?
Nice lesson, thx! Btw, could you promt the PLINK function to find most probable parent for offspring given SNPs of both? (but relationship "parent-offspring" isn't identified, just SNPs and birth dates are at disposal)
Yes. You can calculate IBD with the --genome option, but this is better if you have a larger set of individuals. It computes the IBD between each pair, and the 0.5 or similar then indicates parent-offspring (or full-sib relationships). If from the birth dates it is not obvious which one it is, you have to do a paternity control using mendelian rules with --mendel, also in PLINK
@@GenomicsBootCamp yeah, forgot to mention I have around 70 individuals for search. As I got it correct, while evaluating IBD with -- genome option, should I input exactly one of the .ped and .map file formats you mentioned in the video as the -- file argument?
@@yanketzer5480 well... all individuals should be in one single ped+map file, then you put this as then input for --file and the --genome option.
As a result you get a file with IBD between each pairwise combination, and you could check on the IDs you are interested in
@@GenomicsBootCamp oh, got it. Even received some result (if "0.5" value mentioned above refers to PI_HAT coefficient :). Thank you for helping me puzzle things out! +1 Subscriber :)
@@GenomicsBootCamp But unfortunately, paternity control with --mendel option doesn't work (I used it together with --genome option). Warning message pops up like "Skipping --mendel since there are no trios". I suppose family_id (or any known parentage) should be included to make it work. It's a pity that those moments are not enough documented in PLINK for such newcomers like me :(
thank you , from where you get SNPs dataset !!!!
There are plenty of open access data sets on the internet, e.g. on Dryad, but also elsewhere. I fetured some of these data sets on the channel, see videos in the playlist "Open access genomics data"
ua-cam.com/play/PLdf-U83sN48Mu2x8hvmdwg5TwR6Z_GYhe.html
As far as I know their are 4 nucleotide In DNA - ATGC , what does those datasets means in which they have only 2 character like A , B or 0 , 1. How will they represent those 4 nucleotide??? What does that A and B mean.
Pls help, I got confused 😕
Could please share me your references or the books for this subject? You helped a lot to understand but I need to know more about SNP for myself to understand the whole picture and to for my exam
Hi, the contents of the videos, inluding the theoretical lectures on "Introduction to Genomics" are based on my expriences and work in the field. Of course I got this knowledge from somewhere, but it was through various papers and talking to colleagues and students. It might well be that a similar book exists, but I don't know any reference to point it out.
@@GenomicsBootCamp oh wow that’s actually cool no wonder you were able to explain it so clearly. It’s ok thank u tho for the reply.
Here are the presentations for the "Introduction to Genomics" lecture series (separate playlist on the channel.
pptx-s to download: github.com/GenomicsBootCamp/IntroductionToGenomics
@@GenomicsBootCamp I will read it thank u again truly appreciate it🙏