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Haplotypes and imputation | Introduction to genomics theory | Genomics101 (beginner-friendly)

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Genomics Boot Camp

Genomics Boot Camp

Күн бұрын

Пікірлер: 29
@90MrOlympia09
@90MrOlympia09 Жыл бұрын
Your efforts are deeply appreciated, professor! Such sharing of knowledge in academic topics that don't have huge audience (as much as casual youtube content) comes from pure generousity and consideration to beginner like me, who would really find it almost impossible to keep up with their dream careers without your simplified explanations and tutorials. Hope you always get more successful!
@GenomicsBootCamp
@GenomicsBootCamp Жыл бұрын
Many thanks for your kind words! Yes, we are a "few views" away from level of MrBeast, but that is not the main goal here :)
@ikhlashusein2712
@ikhlashusein2712 Жыл бұрын
I just want to deeply thank you! This is the first time I understand what the haplotype is!!
@GenomicsBootCamp
@GenomicsBootCamp Жыл бұрын
Great! I am happy that it helped!
@giusteliopoli
@giusteliopoli 2 жыл бұрын
Thank you so much! I've finally understood what a haplotype is since it one of those concept that I couldn't wrap my mind around it! Thanks!
@shumuyebelayteklebrhan8466
@shumuyebelayteklebrhan8466 2 жыл бұрын
Interesting and helpful lecture!
@sahanamuthukumar6732
@sahanamuthukumar6732 2 жыл бұрын
Thank you, awesome explanation!
@salmatariq1371
@salmatariq1371 2 жыл бұрын
Great lecture well explained
@softbookingenierie3724
@softbookingenierie3724 2 жыл бұрын
Thank you very much! could we please have a tutorial video on the use of haploview or any other program that we could use for haplotype-based GWAS.
@GenomicsBootCamp
@GenomicsBootCamp 2 жыл бұрын
Thanks for the suggestion! I put it on the list! (The list is long, so no promises for the immediate future.)
@muhammadejaz1269
@muhammadejaz1269 2 жыл бұрын
Thanks for sharing a great emerging complicated knowledge, But practically if you have tassel imputation lecture share a link sir, I really need this
@GenomicsBootCamp
@GenomicsBootCamp 2 жыл бұрын
I have a few videos on Tassel, but unfortunately I am not too knowledgeable about it. So this will not appear in the near future
@saulroa851
@saulroa851 2 жыл бұрын
Excellent content, as always! Thank you! Excuse me, will there be more information about these topics? Since this is the main topic of my master thesis, I focus on algorithms for haplotype inference on pedigrees. I would like to know if you can please share about how to evaluate the accuracy of such algorithms, detect recombinations and switching errors. Thank you, so much!
@GenomicsBootCamp
@GenomicsBootCamp 2 жыл бұрын
Hi, You have a great thesis topic! And fairly complex too! For now, the lecture series needs to be wrapped up, and also after that there is are some more basic issues to tackle. So I do not think such specialized topics will come in the foreseeable future.
@saulroa851
@saulroa851 2 жыл бұрын
​@@GenomicsBootCamp Thank you for answering, and thank you again for your always valuable content!
@adrielsilva5759
@adrielsilva5759 3 жыл бұрын
Amazing lecture!!! Could you please tell us about some of the software you used for this analysis? thank you!
@GenomicsBootCamp
@GenomicsBootCamp 3 жыл бұрын
Right now this is a theory perspective. At some point, we will have also practical tutorials on everything. But everything seems to take more time than expected, so I can not put any dates on this.
@gabrielcerono306
@gabrielcerono306 3 жыл бұрын
Great work!
@Raya7766
@Raya7766 Жыл бұрын
Hi, why don't you have AbC/aBc, Abc/aBC as the possible haplotypes at 4:44?
@AmineMB
@AmineMB Ай бұрын
They're already in the answer (see last 2 haplotypes)
@monkaydgoofy2059
@monkaydgoofy2059 Жыл бұрын
I'm new to all this and your vid helped me understand quite a few things. When I was designing Primers and checking the amplicon in the UCSC Genome Browser, I came across an alternate sequence labelled " chrX_MU273397v1_alt:236887-237284 " . Clicking on it said " Alternate Haplotype Sequence " Could you explain haplotype block in this context coz the PCR product formed has non specific amplifications and no matter which primer I take has the same alternate amplicon. How should I troubleshoot if it is caused due to Haplotypes?
@mohammadj.shamim9342
@mohammadj.shamim9342 3 жыл бұрын
Thank you professor. A big help after I first heard the term "phasing" two days ago. A friend talked about it and said he used Beagle for phasing. I didn't get him honestly. Now things are clear. I came up with the following haplotypes. But in some cases they are the flipped version of your solution does this matter? Ab Bb Cc= ABC/abc, Abc/aBC, AbC/aBc, ABc/abC
@GenomicsBootCamp
@GenomicsBootCamp 3 жыл бұрын
Great! No, the order does not matter here, it is just a demonstration of how to think about haplotypes.
@mohammadj.shamim9342
@mohammadj.shamim9342 3 жыл бұрын
@@GenomicsBootCamp really appreciate it.
@nellysonic
@nellysonic Жыл бұрын
Professor what is your take on using 23andme V5 which is a gsa chip which i read is designed for high accuracy for imputation against the 1000genomes data ... is this a valid use if say im using it for ancestry modeling as it plots me very close to my mothers regular genotype data form family tree
@GenomicsBootCamp
@GenomicsBootCamp Жыл бұрын
Hi, I do not have an exact "take" on this. If you have your and your parents genotype plotted in a data set with other unrelated samples, then the situation you describe is expected. i.e. that more related samples are closer to each other. But it is not a proof of "ancestry" and can not be used to make claims about parentage.
@nellysonic
@nellysonic Жыл бұрын
@@GenomicsBootCamp thank you for the reply
@sebastianzavala585
@sebastianzavala585 2 жыл бұрын
Thank you so much
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