Your videos are a great resource. I wanted to do a project involving neural networks, sequencing data, and cancer treatment and these videos have been helping immensely.
1:00 you will only get more than the expected degree of mapping in a region as drawn if it is a repeat that isn't represented in the reference genome but has nonetheless been sequenced
Thanks for the video! So I've read that short insert paired-end reads (~up to 800bp) are really easy to ligate adapters to (the A and B adapters that you referenced in the previous video) but that longer reads need to be biotinylated and circularized. Why can't use the same adapter-ligating protocol with long insert paired-end reads as we do with the short insert ones?
Because in a De Novo sequencing, you can't know in advance that you have a repeated region. You need both region to be correctly placed in the final genome assembly.
Instead of four bases, let's assume that 2 bases are needed for constructing DNA. In this case, how many nodes (excluding the root node) are there in a tree that store all possible 3-mers ?
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Thank you very much Doctor Rob
I love your videos. Thank you so much for the information.
Wow, I wish there was more of this
Your videos are a great resource. I wanted to do a project involving neural networks, sequencing data, and cancer treatment and these videos have been helping immensely.
a lot of buzz words there hahaha
Thank you!
Thank you
1:00 you will only get more than the expected degree of mapping in a region as drawn if it is a repeat that isn't represented in the reference genome but has nonetheless been sequenced
The title says "paired ends" but you are actually talking about mate pairs.. quite different concepts.
mate pairs are often circularized :)
@@sarahansen6597 to my knowledge mate pairs are always circularized and then can be sequenced through single end or paired end sequencing :)
How does GC content affect assembly?
Thanks for the video!
So I've read that short insert paired-end reads (~up to 800bp) are really easy to ligate adapters to (the A and B adapters that you referenced in the previous video) but that longer reads need to be biotinylated and circularized. Why can't use the same adapter-ligating protocol with long insert paired-end reads as we do with the short insert ones?
is it only me that doesn't quite get the answer to the question in the title of this video? :(
Nice explanation sir.
What is the difference between PE50 and PE100?
What does it matter if A goes to B or A goes to D if the two 2000 bp sequences are identical?
Because in a De Novo sequencing, you can't know in advance that you have a repeated region. You need both region to be correctly placed in the final genome assembly.
Instead of four bases, let's assume that 2 bases are needed for constructing DNA. In this case, how many nodes (excluding the root node) are there in a tree that store all possible 3-mers ?
Six and bus
this might be stupid, but why not sequence between B and C?
Can someone help me understand why does position of the repeat sequence matters? Is it because one might be inside a coding gene?
Well a year has passed, the position matters because we want to get proper information, doesn't matter it is inside a coding gene or not
Thank you so much the same auestion came to my mind 😅
Mate-pair, not paired-end - completely different. One is a library strategy, one is a sequencing strategy.
Still don't know why it's helpful. Thanks anyway