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Mikhail Dozmorov, Workshop 500: Differentially interacting chromatin regions from multiple Hi-C data

Mikhail Dozmorov
Affiliate faculty, Department of Pathology в Virginia Commonwealth University
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30 июля 2020, Онлайн, USA
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500: Detection of differentially interacting chromatin regions from multiple Hi-C datasets

Mikhail Dozmorov (Virginia Commonwealth University)

10:00 AM - 10:55 AM EDT on Thursday, 30 July

WORKSHOP

This is an introductory workshop to comparative Hi-C data analysis. The format of the class consists of an introductory lecture followed by hands-on practical examples. We will outline steps necessary for raw FASTQ data processing in order to obtain Hi-C contact matrices. The principles of joint normalization will be discussed, along with statistical tests applied to detect statistically significant differences in chromatin interaction frequencies between two or more Hi-C datasets. Participants will learn how to change between various Hi-C data formats. As part of the lab session, participants will perform Hi-C data normalization and generate a list of regions with significantly different interaction frequencies. We will conclude with examples on how to visualize and interpret the results.

Moderator: Aedin Culhane

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Mikhail Dozmorov
Affiliate faculty, Department of Pathology в Virginia Commonwealth University

Dr. Mikhail Dozmorov is an associate professor in the Biostatistics department, Virginia Commonwealth University. He develops statistical methods and bioinformatics tools for the integrative analysis of genomics datasets. Through collaborations, Dr. Dozmorov analyses and interprets next-generation sequencing data, ranging from RNA-seq, ChIP-seq, DNA methylation to whole exome/genome sequencing datasets and single-cell sequencing. He extensively works with genomics databases, such as The Cancer Genomics Atlas (TCGA), CCLE, GTeX, ENCODE, etc., focusing on methodologies that aid diagnostic, prognostic, and treatment decisions. His latest work includes the development of biostatistical methods and software to analyze the three-dimensional structure of the genome. He is interested in developing machine/deep learning approaches for the analysis of genomics and medical informatics data

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Welcome everyone. And if you can amuse yourself of this will help. So, This Workshop is called depiction of differential head differential Interruption, Traditions from multiple price eBay t-shirts. And in the chat window you can see something that you can use with start with a brief introduction. Was a few slides and when I get a break or Satori you can see all the resources that this Workshop will use. So let's go to get up early and slides are in the shore.

Okay, so Fuel housekeeping, stuff again, some links package down website, Docker image, and you can start to this Workshop later on using our schedule and to welcome to buy a conductor password. And when we will do this, we're going to use these commands to get rooted in yet, and we can go through the rain yet. Available through package, down websites. And if you open this link, you should be able to see The Vineyards in articles window and we're going to use it as well. alright,

so Couple of facts about human genome, we all know that human genome is Big 3.2 billion base pairs and if you take DNA from a single cell from Human Instead, it will be about two meters long or 6 feet long in the same. Besides the fact it's so long and you know class about 10 micrometers in diameter and this tells you how important for Distributors of DNA to be folded in such way. So it is distant, micrometer Knuckles, and Tails from human body. And they also DNA in statiicz one. After another, it will

take about 500 times distance from Earth to Sun That's pretty impressive. So this tells you about the importance of three-dimensional structure of the Chino and how it folds in. Right now, we'll go on the roads named chromatin confirmation capture technology that can help us to understand three-dimensional structure of the Chino. Crazy. Jim ice report, chromogen confirmation capture technology was developed in 2009 by a Time. Supposed to look at your particular slob.

In this technology allows a strongest and three-dimensional genome structure, three-dimensional, structure of the genome on the genome wide-scale vacations of cremation, information capture technology, but how she specifically does it on the Genome of white scale? Price of data, so obviously is there any sequencing data? It comes in the form of a secure files in the way of a look at it into in yet, but the process to date is the usual matrices, symmetric matrices and see what

you can see on the screen. You can see symmetric Matrix and on X & Y, axes. You can see regions across from someone in the next on an x-axis. Also regions across from us on one in each cell in such Mighty its response to the experience of interaction between each and I are Asian Jay. So search Matrix would be symmetrical around so they haven't answered. I have a note self will correspond to introductions over with itself is built. If you take a chromosome you can split it in show

equally-sized regions the size of those agencies you find. A quality of sequencing data and it's typically have like a hundred or even one. Right now is at a higher resolution data which go through one cable, but it depends on the quality. Search Matrix is not a typical Matrix where you think about rows and columns here, you need to think in terms of diagonals. So such my dicks is around the diagonal of diagonal. View of the data is important because it response to increasing distance between

introduction regions. So it may end on this day, I can do, is there a genomic regions? If you go one step of diagonal, this one step will respond to the interruption frequency between genomic regions 101 unit distance apart, if you go through steps away from the diagonal, the distance between introduction agents will be true, and so Sports. So and if you'll go faster and faster, you can see it on this map. You can Caesar cargo cover Skype kind of faith in the intensity of the

color correspond. To choose their strengths of interactions between genomic regions. If you go faster of diagonal colors fade, which means that the interruption frequency decreases with Whitson Vision distance between in between genomic, regions regions close nearby, they have car insurance of interaction with each other. And if any chance they get farther apart in the vineyard Tri Nam lower chance, interact interactive with each other, and that's important because they decay

in interaction frequency. It's always power, Lord, Minion racing fast. So if you go farther off diagonal is the distance between The increases the interaction frequency between between association's decreases in power law, pressure very fast into this is not drama and dramatic on this heat map because it's bloated in the lock then scale. But if you remove lock them skating of this Matrix, it will replace you. Substantial dekay. If any sequencing data cache and data suffers from my devices, which can be broadly separated entry sequins be run into flowers. Should she

put us dependent this? Like my body is itchy and she's incontinent and technology-driven. It's the type of restriction enzyme you use for your library preparation sequencing platform and other technical artifacts that you might encounter. Someone has a shield East remove size boxes but most normalization methods, they work with individual Crazy Day this year. It's a thick one day this year that the time normalize rich and you would, you would hope his advisers have been removed, but it should a individual normalization. Memphis do not perform.

Well, when one, our goal is to compare data sets. So, if you have true data sheets, think about a relationship. When you have multiple samples, you need to turn on my license and also gives her. And this is what our package does. It takes individual Hi-C matrices, and normalizes is a mature years and it has been shown that such methods of normalization. Your forms. Better than methods to normalize individual privacy data sheets or one at a time that I put on slides 101,

compare different normalization headphones. Best And another are compare a differential detection between between Christ United and also shows at all make up their forms. There's too much disk to in many situations. So, let's talk first about normalization Jones, normalization, of Kai, Chi Theta. And for this, we need to try to understand the concept of mg +. If your work was Michael radiator, you might be familiar with a, my plot, which is another name of it is

blunt and often flood in mg float, allows you to pretty present data from True pricing method is used on the single plot in this plot on the y-axis differences in interaction frequencies so many differences in interaction. Frequencies emergent UI cemeteries in one of my tricks you type of interaction frequency in another fight for my ticks, for the same pair of furniture is in a relationship in shipshape. The difference between crazy day this year should be minimal.

So if you think so, Between are true interaction. Pre-purchase from Fukushima. Trisha's is the difference between them should be close to zero. X-axis show us genomic distances. Where I talked about the importance of distance Centric, view of the date that you go off diagonal and suggestions between genomic interactions genomic regions increases. And its each of those distances, you can see is an introduction. Frequencies have different statistical probabilities. They just have different ranges and perhaps different statistical propitious.

That's why on this mg blood on XX we plot distance. How many steps of diagonal? We go in the ditch on her doorstep. If I go one step of diagonal with a whole interaction frequencies, they use a difference between 7 between true interaction mattresses and those different On y x, + y, + Roth, Those Distant defenses, like a cloud of Point sheet nonlinear regression through it. And remember what I told you, if you would expect the differences between those mattresses beat

minimal, this blue line should be centered around zero. So you're just a, you're difference between mytresses should be zero in this world. You can see it's not centered around zero at all, it's shifted, they need to get up words, which means that's just on a global scale, interaction frequencies in one dominate interaction frequencies, from in Azle, Texas it so it will be always slightly positive. Alliance weekly wine regions here which response to some local biases that needs to be minimized. And this is what's a joint

normalization, Dance, Wii Wii, Fit lawyers immigration through this cloud of point, and we adjust the data in such way. Is that the difference between true beta shirts are minimized? This is what this is, what were yesterday's Nation does. And this is what joint is normalization. I chew it mean by the differences between truth and true high-speed data sets. And they allow us to focus on some large differences in a in a New Direction with Scopes and so smooth beat by Lucia pretty editor. And if you do the same

with methods that can normalize individual Qureshi, latest hits like Chrome o r. I c a r normalization. Is she in well, yes, say normalize individual has your data shifts, but still, if you block them on MD player. You can see biosource. You will swear on the global and local scale. It's the same day or using a normal individual. And then with a difference in voltage on a distance to empty twice and you can see biases are still remaining in. This is what's this paper? When will have multiple facial datasheets.

We do the same procedure it except with a each pair of datasets normalize them. Use Insurance lawyers, normalization, taken us, a prayer of data, sheets and repeat. And you can build trust and it takes about through three rounds of iterations for full conductions. That said, Regional papers, that proves this. And if you work at the mouth with a normalized station and procedures for a differential detection of Chromatin interaction frequencies Here again, I stress your attention on the distance to Centre view of high-speed data.

We perform distance Centric, chromatin interaction G Fitness detection. So, am I trying to look up two conditions in which condition tests reading crickets. That's what you see on your screen, one condition. First three high speed, 80 sheds. And another condition pricing data, since you focus on one particular of diagonal, slice off of this Matrix. So you take off diagonal slice, slice of introduction, frequencies across all three, matrices in one condition and across. All three might be she's in another

condition and you can hear some intro Matrix forms. This is what this transition represents you. Take this Vector of interaction, frequencies in Nazareth, rampant corruption frequencies Free prices. In the regular Matrix are a specific distance between interaction Rachel's. You do the same. With the second condition. You take the slice of introduction frequencies from one might fix another, another put them in a minute. When you care for such matrices, you can apply a standard a standard method for comparison. Open G

strings. Obviously, you cannot use to test because it's not normally distributed data but negative binomial based approach has worked pretty well. So when you can see just for, for this particular, pair of readers remembers that this each stroke and is pumped to interactions between two regions, but for the sake of comparison, with just cheese at numbers here, 7277 a true are quite smaller than the numbers are in the second condition where you was at interaction between pair of regions increases.

In the second condition for this specific, Barrow free. And again this paper tells user to this method is pressure bust a Tahoe, sequencing dips and provide sufficient power in nearly all situations. We can you use a typical tests and we are not inventions will. Here we are using methods that implemented. In HR package, we can use a razor except for compare into groups without covariates. It's similar to Future's exact test or we can use generalized linear model

makers in. Those matters are useful when you have Kuwait, it's it's like you're somebody applicants may come from one batch of the day that somebody may come from another bunch of the data and you can create for such, but if you're using generalized, linear model framework and we will see how it looks like in real life. Intuit Santa will come to the final part when will the tax differences. We will meet you interpret them and 595 interpretation steps. With that

we could come up with so we can visualize differentially interaction regions. We can be fertilized with using men, second line like lot. Remember if you work with data on Creative like Lord is Snip spoken out of the genome Zoe, the same concept can be applied here for regional migration across leniency know. You can put the number of times how this is a number of times has been detected the interaction with a nursery. You can also upload the average. You this region has been detected

SD Financial interaction with other issues. So this woman cut them, like Lord allows you to see which regions has been detected as frequently differentially interaction. Second part is, if you have, if you have gene expression for your samples, you would expect that. There might be some changes in gene expression response to changes in different city, Interruption chromatin, reach flight promoter. Thank you like famotidine cancer, interactions or disruption of the Polish people Associated the mines and we can look so different for

the interaction directions overlap with different reintroduction. Differential Express jeans. Some of the way you can you can make a hypothesis is that eventually interaction, Regents change some jeans, Zack response to a specific pathway or function and you can test wizard, skins, OverWatch in, differential in traffic, collisions are in reached in Colonial Parkway, or share a common punch. The last two methods involved with the power of boundaries of the biological Associates at the mines and

into proteins, that are that are Mark, Mark with the boundaries of the Fellowship of the associated, the mines, at the associated, the mines are regions in the genome that are highly self interaction. So 1200 troop, Edisto Street in Des Moines loss of regions, interact with it. And in a Serta pillows, Big Lots of Greater Des Moines, lots of reasons interact with in it, but they don't interact with each other such you search the Palo Alto College results within the mines are separated by boundaries in the world except the interaction

regions. Make respond through this and start boundaries might be distracted or newly created so you can test for order love for statistically significant overlap between boundaries of the fellowship. Perfect in Des Moines end, differential interaction ratio. Insa bondage of the biological Associates in Des Moines, have been shown to be marked by proteins. Like ctcf insides 21 and members of vacation complex. So is there a difference between a check marks that

might be in reached its dividend for the interruption regions and we can test for oil for statistical. Significance of overlap between the interaction regions in binding sites of different transcription factors or Houston marks or methylation organism sensitive sites. So on this I believe you're with somebody that the distance Kendrick view of high-speed Data East reachable info for these. Remember the concept of mg plot? George Floyd normalization, removes between data

shift biases and it's implemented. In case you can buy our package. And differential analysis, considering distance, a Facebook game of their phones. And it has been implemented in March because she compared to package Obviously, this board shop has lots of material to cover. Everything, keep in touch or ask any questions as they're in chat window or anywhere else. Get in touch with me. And I will follow up open issues on one package pickup, repositories. And

right now, he let us go in and starts starts with a by conductor station, you should already be familiar with Workshop. Don't buy C. Cancer, cancer data, scientist. Org. Alarm starting this week, might be good. There's a lot of questions that you have necessarily true sub sampling leads from the true crisis that has yet. So they end up with the same Library size. It's a great answer is no because this is what what Louis irrigation we'll do is we'll fuse at 11, Matrix is kind of dominance

here you can see he's at Rimes centered approach madly around 3.5 and what is your reaction will understand it. When you adjust the data is a date that will be interested in sexual differences will be minimized. So it's a global defense will also be minimized. It's a great question in. This is pretty much how the idea of Isaac Stop it ruptured, This Global and local biases and we have been thinking about the simple way to remove her. So this can be Done.

Can you explain, why is the difference between matrices should be Zero from, from Aaron? He sick X and Michael right times. You have some sense of jeans, in the case of high-speed Data Book of Psalms on soft interaction frequencies, we wouldn't expect a safe search on changes but wouldn't expect like such dramatic changes that will change something else unless it's a cancer cell, which cancer genome, which Gene and completely disrupted. So it's it's an expression when, you know, my lights are nice. You could

you try to minimize their differences between Zone in focus on the Romanian changes which most likely Lopez punch through. Biological defenses. Dewinter chromosomal interaction. Also cure and how to analyze and visualize results from interactions. Are infrequent, chromosomes occupies, their own stories in a typically don't interact with obviously in cancer. It's not true because enter promo some arrangements happen and in turn, only the loss of interpersonal interactions. Intensive Care, Unit true count for it Fried. Chicken prayer

and multi pricey compared cannot analyze in the chromosomal differences and be simply because we are we need to consider Square Matrix square and symmetric Matrix. Seems different chromosomes are from different lands, some of my tissues. They want me to make my normal eyes because if your tags are conceptual with whilst you that be square Matrix except it will be a huge. Well obviously this confidence Joel a very framework HD 2500 454 must restore big data

so that's a matter of future development. Falcon we incorporate information across multiple Houston scales for example, of deception of options because lost over smaller that and thank was in where we are. We are incorporating in from a Across multiple Keystone skills of these MD, Florida allows you to focus on Just Dance Centre differences. But the question is more about you stop showing off. And if that's are disrupted that's a different story for for this with every other

package, which gold. That's complaining our package. It's also on bioconductor right now, Stephen development the ocean, but this. Compare package specifically focuses on the Campari boundaries of touch unless you separate story and matter of the next Insurance Workshop. Does it means it's a decrease in contact. Frequencies of diagonal biologically means that it's rare to see distant parts of the chromosome. True interrupt is there typically every Houston sis.

So yes, if you go farther off, diagonals, interaction, frequencies grow very fast and keep it cordial. And people can see the legend true megabass distance between interaction creatures are still biologically relevant. So I've been some preferences, a troll, some long-distance Hoops, intersystems long-distance Loops by typical biological distance, it's true Mega bases in terms of unit distance. So, if you have your data at church and you can count how many over there, the most steps you should go

to reach this true megabass. Plymouth and true megabytes is also typical size of a maximum size of the baggage car. Do you think it's possible to use this approach for inter-species comparison such as human and mouse? As soon as we can? We can mop in Jenny, Creations between human and mouse genomes. This would be possible but it's a matter of, with different flavor of efforts, and not feasible at this point, but this would be extremely Okay, now it's called are statistically test. Will come to this

house. How do you say overlap of differential, Express jeans and eventually interaction regions? This is Donna, using permutation test in veneer to detail, which we will, hopefully come true, it's corporate. That's we talked about Compare conditions with replicas. Obviously. Yes, in this is what multi-phasic compare does. In this is what the blood shows. This is when you have multiple, but when you have multiple high should be this year, it's obvious, you have more power. Aunt again this is huge and HR never does this work was

gone as well as if I should date. That Martin is you know what? You're trying to send me contractions. When I see no white scale, it doesn't involve ligation like if it's okay. I should data and as soon as the date that is in in the Square for a month, for each year for each chromosome. Yes. It's not a problem. But for gum you need the specific three processing steps to extract data entry or a matrix 4 months. Is it possible to compare interactions without their players? So, yes, it's

possible to compare with and without, without is fine, she compared compared package is for comparison of two data sets, was out there. The price, you pay the shift Swizz Beatz. So does this work for for detection, a b compartment changes? If not, would you recommend any tools in the compartment changes are able to compare. If you're able compartments is additions in between them, Chris pungent, root activated, and repressed, parts of the genome compartments are detected using principal component analysis plus some of your vacations. But basically, you can

extract the first principal components from my trips to composition, and compare themselves, just the numbers. So, if you take the principal component of numbers, keep a particular Sports shoe compartment, a sign of the radius, Chris Paul shoe compartment be, and you seem pretty exhaust Victor's. Those letters will be if you kept your day that it's your, it's your tone. That is a Lucian like them. you can't repair number, whether the difference between two vectors

off of numbers through the defenses, And say yeah, that's straight forward. In terms of how to do, how to do this principal component analysis on cuz you might receive packages in terms of art, I believe it's hid. She hid. She our package can do it easily and loss of those, which one can find any Security. In fact, so easy to do yourself. If you go into compartments by doing principal components, on The Matrix of relations, So it's pretty straightforward to do just in the plane, or is there an intuitive explanation?

Why you see those nonlinear relationship since OMG plots in the only internship. Explaination is there are some technical biases which we don't let them throw off and they are always different in that just has there been. Some date is not perfect in case your data is quite large, it's about twenty times larger than typical so it's hard to know what went wrong and why by society's are so they always give them hints of the variable when you can throw up from Houston, sister will be considered handsome. Man is a major issues and it just finished an interruption

region test. So probably this question for response to the point. When we, when we go up there. So if you can see the release of the next say, it May 5th. Thousands of empties into this Matrix, thousands of rows in this case, but if you go faster of diagonal, you obviously, you have idiots and this date is already and you have just one empty. So how do you use this? Because it's those distances you have insufficient data to estimate. If you need our papers, we introduced the concept of progressive food in. So it's

imagine it works like that as if your distance, you just things that are excuses. If it goes as you suppose. You think the second place is the next and if you bought father in Father of the heaven, owe you more and more data. So it's actually you pull this data to Yes, sir. Remember powerlogic a will be approximately the same, the gate. So, this Progressive pool, and allows you to get sufficient today, to Tribute to solve matrices and estimate parameters off negative, binomial distributions need for differential analysis. So it give them a a b average

man from is Citi Trends in between them, sponging through activated and their priests places in which you know this but true that slides this paper introduces them and it's pretty straightforward strongest and obviously not so into what this word, leave them on Titan and others found. It says, it's as simple is doing principal component analysis and design of principal components telephone for each region respond. Whether this region is actuate or a priest in San Jose, in the compartments, to respond to True like a take Apartments response to a

higher density of jeans. Lots of Houston, activation marks and be compartments response to Regions like running the associate at the mines. So any chance of heterochromatic So if you think about you and Sheryl Crow matching, this, what's, what's the response to? How do you decide on a bean size? It's a whole different question. It depends on how many, how deep is your, your library in cold. What is the quality of your library? So, children crafts guidelines into. You can reach me. I can point you to exact street estimated

approximately 600 million reads about 10 KB. So what is it necessary to stop sample? No, I know that's it. All right, let's spin it. Spin our instance and I will die. This email address you can use for for contacting me. I can copy the password and our studio will be our username into it will be using them as well. They didn't yet which we can look I wish working who can Art Studio. And it takes the second but it should come up in. Before it starts. I will just go through The Vineyards briefly bunch of packages in the next. Actually, we will talk about how she dated 4 months.

So as I mentioned price of data comes in a form of, for of sequence, Reed's store in Fescue format, inspired into place in trees that are several pipelines that can be used to process. Why should they done? Rstudio ends our password. Is there a multiple Deuces at 10? yes, it is God's chosen yet because that's the most simple and informative format and get you through some major issues, which you can use in our ends in, in this, Winona Lake in True. Detective defenses. So that's why she and

Dot all formats. They are typically filed four months output by and Five Lights. It is. All right, is a four-month produced by the juice and Pipeline and. Old are produced by Hi-C Too Faced lip package developed by near me. Love those are strong zarathustra results, 4 months back and forth. Public data shows are available on our website and on this FTP website in t you can download lots of data and play with it. I'm more about data, formats are in The Vineyards for our packages and I will briefly

mention that the typical format is square Matrix, and buy in Matrix. Until I would you describe but it responds to Regions on X and Y chromosomes. And this is what you see in this Plot In Color, intensity epistemic. So contraction frequency between responding features and then you can again she's very intense diagonal and S you go off diagonal or straight sew in production frequencies DK. We can actually do it in our studio and then our studio. If with type There are multiple ways to get rooted in yet. One

is simply you go to packages and search for Heise Heise compare Tropi. It's it's this one you can play and you can get through Nazarene yet here and this will be living yet. It's rather convoluted just dive typing in the wrong place. It is the name of the package. And this will bring you directly to The Vineyards and you can get, you can get a Caesar or cold or sore, sore energy source or savini at itself. We can look at it as a files, you should see the receiving your folder which has a file which will weaken

the use and let me make it. So it's more, it's more reasonable. So what large city is already pre-loaded was opaka. Just I just ran this cold, shank true Lords or packages. You put the alarm. Okay, now it seems to be running. So again, I already talked about scratch and ate the four months old, the date. As if you need for the workshop is packaged with the workshop. And in particular, if I love these battleships, which is, which is just pretty processed data

and Luca. That's why I keep my boyfriend when texting all Reggie Square Matrix and I am way too straightforward strongest and and analyze. As our data types are in X and plus three waitresses. It's also an X in Matrix + 3 additional problems. If I run this right, we'll see how this where do snow cones look like it's simple modification of NBN format to explicitly say what is chromosome start and end. It's the same genetic Matrix you can see is a diagonal. You can see somatic numbers

across that. I have so great, a great photo This data is not where is Sparks, Sparks record my place. My tricks. That's the most frequent format because Imagine by in Matrix shoe store shoe, store is a full Matrix. In a text format, give me a pic if you know one of you can reconstruct the other car. So you can start just the upper portion of this Matrix. And second of all kinds of data is sparse, especially at sell, watch Archer of diagonal, steps is in production, frequencies

are rare, and most of them will be as Heroes. We just don't need to storage Eros because if their mission, we can reconstruct Mission zeros. This brings us to the concept of Sparks record Matrix. And so pricey compared to provides function to convert between the full Matrix. Interest parts for months and vice versa. So I will take this food for my headaches and can drop that response format so you can see how sparse day that looks like. And it's pretty straightforward three columns

for the church. This Matrix is chromosome specific, it doesn't have chromosome information. Because by default, it should be forced for specific chromosome. In this case, we are using chromosome, 22. And Sarah is a first edition coordinate, genomic for genomic coordinates of the second region, ends Interruption frequency between them. So that's precious three Fort Worth August. You will need to know that his Illusions the size of the association's because this is a start coaching at of the region. With the end, we need to know what is illusion of our high-speed data

through the process of obtaining, the day, the in-processing this week and we are not doing it. Let me see if I can if we can go to The Vineyards. Into it and actually look at it. Is Randy Orton in a nicer format. So, this is where, where, where are in a in a mg. So probably is that a lot of problem. Betta in a gym on Street, which command lines, should you use to download the data? We're not doing this because it's rather time-consuming. The data itself takes about a 32 gigabyte of data,

but the package contains a small store exception in this data, which you can download it comes into. Qureshi for Extract data in text format. You need to listen to call straw. And stroke, can be downloaded from heat up repository from either. Love in this case, windows from Linux version as well. I work on Mark and when you download to those crazy fight at files, you create folders for them. And do you use this? Throw function, stopped, non normalize data from the sky, C5

files for each chromosome for each chromosome. I am I in the loop at resolution. This is there a solution of our high-speed data, as you can see, it's very rough. But it just was a demo purposes. And you say, within the chips for how much is a Yukon View Inn in Chester Jester? You can also extract the data for X chromosome and repeated for 4 oz of samples. And when will you have this daytime we can load it into our. I show you. How was your day today? How's the folder structure looks like

And when we come to load, your Illusions are data. We specify which chromosome over one Trooper seeds, we proceed with chromosome. Chromosome one, we use for samples. Here are the names of our four samples. Would you find the resolution? Would you find a different list to store samples and chromosomes and Inns affordable weed is a beta and collapses in a sample list. This is ours and I will probably, at least you can see, is the date that, which is very similar teaching on the

French chromosome. Chromosome, start is this party supposed former to do? Is chromosome, start working at 3 session, start coaching the second region, and interaction frequency in to this. This is the least populated for its intense interaction frequencies of all four samples. And when was have the simplest, we create Hi-C or Hi-C expression Orchard, we provide the data list and we provide groups, remember we care for samples for this type sample was specified. Samples come from from

church group in the second pair of samples come from. The second group. This is what we do. And when will look at this object we can see satisfy she experimental object, which restricts betterment Brooks and you can see what's inside it and then cybertooth Pressure straightforward way of looking at it. Again, Sports Forum at chromosome for genital region, II reaction distance between those two regions and interaction frequencies for all four samples. So it's just a form with $34 an hour later in such

way that it's possible to repair form. Definition expression analysis that looks like on mg blood when it comes up and you will see, you will see is a beta obviously comes from from the same loves the same sequence in. So the biases are minimal but you will still see some in this fastlove function. This is what we can look at this is Carlos. A date is the date. That looks like. They are so simple, Explorer, tan, MD plot and you can see is a, some samples show some deviation not much, but it was Tuesday are normal, guys. I'm using voice recognition

is pretty fast and after after you lose, it is a date that will look much nicer. Those biases will be gone. And after you normalize is a daytime So, it is a Nathan with Luke. Is it as a day, that will be interested in. Let me see where, where, where are we are at Thai, mint? I will the stock short. Shortly. I just want you to know the most important step of how you perform differential expression or not. So, when is a day that is normalized, you can see it's perfectly

centered around zero. So she gives you answers are minimal and business hour of where we have groups, Define and Sqaishey exact test will be informed. If you don't show it in differential equation, and it will take a few seconds and then we can float it. We can close our differences, using mg composite function, and it will it will float the same mg blood but was differences. What's a wisc? Our differences so is the most significant differences of his most significant revenues will be covered and differences with this significant to be where you swap the car color to yellow and

nonsignificant will be cowards, will not be covered. We also specify G. Range in this, Chris Paul shoes. One of the question, previous came through, which gentleman of diagonal distance. We should look at you don't want true across the full range of Distances, keep it going to look for film theorists 40% of distances. That's what specified here with chromosome 1. In India. This is how you perform basic differential expression, analysis. I only want you to show how differential expression analysis results look like in 3 seconds.

And I will look around this. Command is well in It meant, you could show them possibly in the vignette. It will be nice and colorful. So those are plots that we have seen and yes, hear our house. The difference of look like, it's again mg plot difference in. Yellow is less significant but still significant Andreas are. Yes, you would expect larger differences. Have higher chance to be that you still pretty significantly different and this is how I was at his house look like for each pair of

region region. 1 in the region through, you can distance, you can look for change metrics, housing, tracts and frequency between those regions changed. In this case is not much and you can see is a chance to email. You is not no different with output statistics for over each other. So you need to feel her by. My phone example, you've been seized at 4 display refrigerants, adhesion set, start it and this gorgeous. Since it is a second edition, starting in this court and they have distance of 3 units,

frequency decreases at least - low, my local change if it is sponsored through accounts. But in this case it's every interaction frequency which you would expect a similar interpretation is our nation, it would expect. The sapphire is a kind of cheese is a more changes in. It will be biologically relevant and again be radio interests of the radio which is your stats using a VR So what is your straightforward interpretation? It has a lot. We first went through one, sort of 70th and we are at time again. I will look at it right now and please

reach me out later on. I will be happy to talk with you and response through issues. I copy any questions that we don't get too into the slack channel is well for you. I think all the questions are in the pools at time. I think And I'll copy them all into the into the yum stock Channel. Post. A link to the slack channel in the in the comments for everybody. All right. Thank you. Thank you.

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