200: Integrated ChIP-seq data analysis workshop
Kai Hu (University of Massachusetts Medical School)
Julie Zhu (University of Massachusetts Medical School)
Haibo Liu (Iowa State University)
Jianhong Ou (Duke University)
5:00 PM - 5:55 PM EDT on Tuesday, 28 July
ChIP-seq combines chromatin immuno-precipitation (ChIP) with next-generation sequencing technology to analyze protein interactions with DNA. It has been widely adopted by biologists to identify transcription factor binding location and to map specific histone modification or nucleosome position on the genome. A typical workflow of ChIP-seq includes experimental design, sequencing, and downstream bioinformatics analysis (main challenge). This workshop will focus on the bioinformatics part by comparing popularly practiced tools, their advantages and disadvantages. And an integrated Snakemake pipeline, which wrapped around selected tools, will be leveraged for the demonstration of a sample analysis.
Moderator: Mikhail Dozmorov
My areas of greatest interest include data integration and data mining of high-throughput experiments, such as microarray, ChIP-chip, ChIP-seq, RNA-seq, miRNA-seq, iCLIP-seq/HIST-seq, ATAC-seq, and so on, for transcriptional regulation and post-transcriptional regulation. I aim to develop and apply computational tools (R/Bioconductor package) to analyze and integrate various data sources. I am engaged in projects to discover transcription factor binding sites/motifs, and correlate the presence of these sites/motifs with RNA alternative splicing or polyadenylation profiles.Перейти в профиль
* I am passionate in integrating my solid molecular biology background with the increasingly important bioinformatics to improve the life of our human beings. *I am currently looking for job opportunity outside of USA.Перейти в профиль
Welcome everyone. Choose our last session and we fear for speakers and I start with talking about integrated strip, she could date on Isis Workshop. Thank you very much for having to see her. This is my first year to attend to this meeting. Thank you again for attending this school shop from 5 to 2. So, before we get started, you can choose to run the Bookshop. I think you already wait for me, there with the procedures, we can either choose to do one little
shop on the cot. By clicking this link here, I've already posted the passcode, so you can check out their shop locally by downloading eye. Doctor image, software's essential for this. So we can carpool. And when the doctor image, All set to go and wash up and figure out. The more detailed instructions on how to run to her image, you can go to Mikey have page drive by the house so we can check out entangled. There. You can copy and paste the URL and old clothes, from there. So you don't have to text me still here. Is a brief
outline of the bus route today. So first of all, I would be a very high-level introduction to talk about the concept behind Gypsy. I've also talked about the commonly used tools for a like quality control with my pink as well as reporting procedures and the focus of. This one is out there for all of them station Parts. I'm going to talk about Monday to our packages for the village will Edition. And one package is cuz I know there's a package cart and most of the two packages were when they developed by Jeff home and Judy and they are also the
co-author of the book shop and of course, at the end of book, shop are going to answer the questions and fifth grade to Close to You by the pool. So I guess I had this one. So what is chipstick Mexican Steve from the start from here, to conduct your steps and seek him here, represents for the chromatin immunoprecipitation. A specialty to pull down the DNA fragments in 64 Oz. And especially as being was first proposed back in 2007 and quickly as the Bandit the ancestor by chip chick specialty. And I
found just over the last Almost 2 decades to analyze the DNA size for interrupting proteins as well as a combined with other type of day. Like I said, they have also be used to infer that she works with all other techniques is far from perfect. They're not a problem was Gypsy. And one of the big problems that I think it's about the high for Spartan Race. So therefore to ensure we have the best outcome from 50, we've designed experiment, I suggest you to follow the instructions over by the encode project. So here are they still several suggestions that are supposed to be in
Qatar. Well, you have to, you have to have a so-called a chips with anybody which have or high Affinity to The Binding protein. And you should have at least two biological weapon, kits for nurses. And also, don't forget to prepare it, mention controls or the sample. In terms of the shipping, depends on your glasses before the transcription Factor ship sicknesses are 15 million race circuit, mini trees. And here is another super, super simple version of super slow. So I
asked you if I met. So the first thing going to do, if we receive the fuk you follow, is to perform some matching procedure to map, to the reference genome and create a pencil. And then after you have a penpal, they're going to come, you're going to run time to call her steps to generate the pig information, with our start, in the bassinet. And of course, as you can see, from this Buffalo drum module for the control stat analysis, and there are a lot of tools for pain control in the market. So
to name a field to C&D pools at one of the most, is that you coming to use before the focus of this shop will be out of the downstream and is therefore in the demonstration. I'm parked at talk about to piano. Antrim River has two packages before I dive into the Duncan that says more about nothing and be calling procedures. So, for the mattress or stickers, over the years, like in the past, two decades people have developed over 90. Different matters, here is so different matters
that are divided over the years. And this this matters can be roughly divided into two categories according to the end and that compares different aspects of the lepers. So, here we would recommend using beat up a little bit of a liner to put on the man, that just because that WWE has a very good compromise between the matching Precision, completion time, and many other But what if it comes to that the color is more complicated because depending on the amount of your target Trucking, the Titans to the profiles, can people from each other. As you can see here from this
for transcription factors will be very sharp and tall as your dear Where is the 401 fiction chips? Takes the stakes. Are you are a very broad. So it's changing the color to accurately a sign for people's neuroses and in reality, different colors are specifically optimized for different types. Of tools. Are there for pecan steps. For metal case, we would recommend using nice to Forte colors that, but for the brother Chiefs would recommend using feather for the pecans. And after you called the
police that the cupcakes will be. Starting the Baphomet Baphomet is simply a test on it, which stores to take calling information. As you can see here in the best out contains the information, so you use so that are required from Aunt because this or columns are essential to document the provision of a pig and you just have to look into the applications for different eye colors. Other columns represents So now that we have the NFL, The Next Step would be to put Humpty Dumpty, molasses do to this and depending
on your specific research, call the first and are you ready? We have time is imitation of the pics. You still want to come and try to figure out what you going to do next. So here I am trying to Sunrise all the commonly practiced passed into 14 eventos. So I will talk about the first event. Those that are cheap with a cheap piano package. And after that took over and talk about the check Beaver, which covers the next six. Even those So now we can move on to the Temptation Park. So for this part, you can go to the BX
where I also shared the link to The Vineyards at box. You can just copy and paste the URL from the fiance's pretty comprehensive which contains a lot more details of the oven yet. Okay. So probably the most important. This is the first of all I was going to talk about how to use your piano to perform pigmentation. The bicycle is it. You need to put on this for her cuz I can see of steps. The first of all we have to redeem the pick data which is in bad form and converted into inches. And second you have to also include to the
images of that you're going to do sanitation. Picking bash function to end his computer connections between the pecan dentation. And finally, it also tries to add additional information to Anthony file by using the edging ideas. So move on to the first step to reading the PayPal. So here I tried to use the example data that is stored in the attic and no package. So you can use the system file system. Has failed to locate the past of the example that is stored in the package
store in the package and then you can use the Avengers function to convert the file into a range of subjects. So here is the file formats has already made it. So that's what it mean to be a human just object. so after we have the pizza in the human subjects, the best time is to read in Egyptian Palace, and converted into, so many different sources on kitchen towels and assemble a hero4 session, but use the uclc It's a shame to damage has a function that converts the internet passed into a gibbering, Texas from here. So after it, sat for two steps, we have
both the people and the ancient Palace in giving up yet. And then we can, I use a note 8 fit in Bosch function to try, to abuse the connections, between the application and the pic. I said there are many more of us for this assumption that you can't use to tune the way, how you going to answer the pic. But here, I am only using the default printer so I can look into the documentation to see, like I might even other furniture for them to process. I hear is the result is also a human subjects from the
First Column to the column. This regions represent the information from the Fisher column to the last column represent information that has been already linked to the pick. So because I guess I hear what you saying the it here under the speaker column represents the entrance Here because I guess you said you thought. So before this, the nearest location and also choose to add additional information by using admin ID, For me, there is one caveat is that when you are using the cfpb and patience, you have to use an SSID for the future. I detect if you are using online, do
you have to replace the entrance idea? Was to unplug watching ID and supply house. And you can see that you have another extra Colin musical symbol supposed to have a travesty is pretty simple to use. So the fencing that it's my first of all, you have to redeem your house using a function. About here is a picture of how the picture is in heat range of subjects. A function key used to deal with that and improve the to take list. And he'll get the results it also
in the shop yet. So, as you can see, the first over there to pick it, actually comes from 361 is from the 1/2 hour from the jacket to that. So, we also choose to make a Venn diagram to show the overlap cakes. Like between two friends, besides Nick, Venn diagram, Venn diagram Another important question that people ask me is like what how do I select the officials to benefit from the price of beer is the distribution of the betting sites across different
pictures and I'll be caught in the previous event. Hope I hear is the results shown here. I can see that most of the pics are assigned to promote the region and ask for, it is possible for a single Peak to spine, multiple pictures. So address, at Mario's, give me ask her. I wish and wish official should I assign picture? You can use the president's argument to try to determine the order of education, is at the beginning of the 4th are supposed to come over and other features
like maybe wtr the pickle only be assigned to the prime mover is that a car that's the function of the prison. Nucleotide level view view. So if you sign that, you can't go to true because I'm the chief to all features, right? Okay, so the Nepalese employees to try to find pigs that overlaps with bi-directional promoters. So factors promoters are basically refers to some locations that are between the chest against our sights of two adjacent teams that are transcribed
in opposite directions. So the battery came from your jeans on the other direction to find the promoters, who can Leverage The Pick 3 p, e r s r with pearl and Piper. And you got a five is about multiple nurses. So busy here, trying to get a summary of us. Go actually we have a lot of a message from the ship a package and then some other fools like me more homework to try to perform. Do you want me to search a multi-nation? Alternatively, you can also use summer is kind
of a pig's function here to try to test the predefined and see if they have a hearing this Workshop. I'm going to show you how to use audio summary function to calculate that this forest for all different potential audiko. All different eyes and then try to be right back. Okay. So first thing you still have to get the softer sequence using the cat. All people Seekers. Just apply the function to the Olympics object and you got the fact 2017, the stick object
variable, and then you can try to Sunrise the multiplication using the article summary auction. So and then stack the fact of your lies, the Maldives that I can tend in the fuck you, fuck yourself from here? And another common tasks that people going to try after you answer the pig, say, trying to prevent an arrangement classes. We have provided another two, other have full function swine's. Call Cathy Brisco. The other talk got engaged. So let's to apply an image to Uncle. Be over left and fish until she
turns out to be at the printer here. We have multiple sets of pics. It's also being very interesting to see whether those pics are committed to each other. So we are to see whether the pics, like a cricket retailer. You can use I'm still take a test to. I should have said go ahead, use the hyper geometric, make them diagram option to perform this forever for hypogastric test, you have to ask me the number, the phone number of potential body size which can be very challenging, a heart for another. Therefore, we also develops another test
with the written test. You don't have to ask him if the potential total number ahead of time and just apply function test and see whether the pig are connected to each other. Do too, before you performed a population test. The first we have to do. You can choose to remove the hot spots that you can just answer here. And after that, you still have to download the pool information from you, or you can get the full formation from the encode project is to San Jose. And after that, you can just apply the pig, perm,
test on different sides of pig list. And here is the report on the left, the black line represents the expected and the Commission test, whether therefore we have this poor I'm going to talk about. It's about managing finances. And we both sides of like people supposed to print transmission, doctors very nice, the Penningtons. So, under such a scenario, you can try to use the picture or something to realize the messaging for different cakes. Before you do this, first me to extract a signal from the chicken using feature alarm
signal function. And after that we just applied, the land is my land. If we can raise the brightness of Jeannie and profile information with Fisher a line distribution function. So I think I I finished the cheapest kind of Temptation. So next I've ever give it to get home to talk about the check. Remember I have, I don't have enough time to cover a big package, lollipop on the timeline, for my salvation, on the mutation beta phenotype change, the results of our nation
Indian reservation, for example, of a v m, c is a methylation of the five positions of the Saints team. The DNA methylation can control transcriptional expression, like a single for retrievers will recruit some part in complex. It's will reprise the finding of a RNA polymerase, rtfc which in turn, reprise her. If the promoter region of the tumor suppressor Gene is a mass of 88 and shown as a hypermethylation, the expression of surprise to you, be eating regulated which in turn leads to
answer of Heaven. Black Yoshi has a Janome browser Washington University program at Regional me. Brother. It is a also show the different regions for ICC is find me location. Location is basically on India's the spelling of a DNA segments. Find me location, tracking song, location on the Covenant bar with a relationship or chromosome, mutations Edition, duplication YouVersion the substitution device location on. Find me a reason why we call you down. Will human Cosmic database on. Like the only browser to be patient under TVs need for comparison of
title, belt region but also other species. Beyond the online tools. Are there are many tools to create a new location diagram methylation locations for multi cica. Require a special tablecloth to call the lollipop on needle person called all location map her and lollipops. There are so many courses a wild country or falling for it is very convenient for publication is a very powerful tool handle height and size of data in bad database that is to say your niece will prepare all the way down by yourself. We shall file by file
an application. On the mutation data to X Factor auditions that, you can use on cats TV, online, result of the combined events on the tenderloin for the for Highlands events. Truck dealer, also, combine the coverage for the Wiz integrated part is a highly customized. For example, you can customize, the limo the symbol of a caller score against asking ball, python are even the ship. Univision Williams Elementary in the allocation of the original shining package, the application of a villa is available at this
page today. I'll have you in our show, the app you'll come get him more information from the video. So you have a publication, here are some examples for Publications that people using truck dealer for shows that the female in the drive. Be to go to the author of the lollipop stack real to represent Snips, that you different patient and seasonal color and Amazon indicate, there is a number, you know, details but not easy, either? Right? Before you go to the author, using the color to show the base while you patient.
We can go to the big Nessa. Is all the examples for weakness. You can get as a weakness in this webpage. A real zombie. So, you just say a dress. Yo-yo, gas station. Flagstaff house at 202 Garza. Reverend Sophia. So I will. Max Mara sza. The truck when we go to the beach country, produces several staffers cup recall as a location data on my solution. Date on the second is a prepare for tomorrow and then to call the Bulldog list. Yo-yos videos of school tool to indicate. Indicates that the
lollipop lollipop the color of the law and the father of Futures videos of cheer answer objective observation and has all the information. You just keep five, stop rotation and hold position and has a few color. Teal color on the highway when you talk to them. After that, the okhrana is a example of intrepid or extend videos, Archie model from checks, db2, extractor and location data by lollipop cost, under your data, from a band, called bad file, or whatever, from our translator, all the
stuff that you do. I prepare as a komodo. And the sad is a caller the symbol something like that. So the poor chap who see how he says the plot a backup I so you can see this is the form isolation. They have, you can probably that massive data on a message via, we also show the idea of your lungs photo cell. And also only time to see how is an example to show. How do you know, the price that they alter to call some of the data for my patients are different patients,
because Are you a big heart? A spider. A caterpillar caterpillar. They also assign additional metadata in your gifts. Alvida find this color name as a society, you can talk on Bolton. If you'll see a sign a title, top individual pausa about the transcripts under the transcripts, If you want to show you a small side speaker, you may want to fight and Baseline Mesa using, fun style is a fun. Then we we Plaza for methylation data as well. Looks like the height of the thunder lightning.
So I can get the lollipop to show the location on Snap location State. Her we were lies a regular race coverage app is it can be easily integrated into Standard Time for dating sites, such as a chief, Stephen osita methylation, seacourt University application and would like to send out. I'll come back after 2020. I took us to see about that ship. You kind of restaurant is like, how the function besides a piece which overlap to Mother one dummy region. Respect me if I'm not if I'm wrong. So I think there is a
parameter that you can't ruin too. Try to light a sign the future study want to. So Yes, it will more than one genomic region. As I said, before, I signed into my Nico sign a sign in the prime of her, say I'll leave you a computer, ask him first, there is a crime in Texas, Appliance solder of the ones there is only one region and the older you are fine in the sanction. Okay, so fun second Quest how to do with a PICC getting associated with multiple genes. I'm not pressuring her stylist and your
dad's a crap. I know Haitian depend on your experiments that you can use to find the nearest got to be lonely. All codes. The nearest I no tell I no tell I no patience for you. Is there a magical Regency Regency yokan. Marvel future fight, whatever Avery, jeans are designed Max cab, you can order for you as a method of promoters all funded the apple and the nearest Nearest, computer supply directions. There are a lot of them Prime on her so you can sign for the gym bag. So you
can read the documentation for that interview, for example, for you. Also they trained us. You can do try and do the scientist Simon. If you only interested in the same strand with other patients and you can do that too. And so like a champ on Saturday, I'm pretty much let you know, so that everything I just want to make sure that, you know, because some people are. It's actually a can And also the kickstand pizza and then I'll pick Center. And I know the feature style feature and pick up my dog, you can pick all this stuff onto
parameters as sudden and so usually people interested in yesterday and buy some people interesting. And I need to use to display and on any features in the region while fall on 5 k b, a n k b and then you will use it over that. You might have missed something you maybe want to be including both, are you confused her lighter using? And I'll put the beta for example. And if you want to keep, you know, you know, later are you say, oh, that's too many things. I saw in the officials assigned it to you can
feed her using like a distance. A feature to the feature, to the nearest, a star size and distance. And to Seattle later. You can always look at the menu and you always says, welcome to post a question to support site and Will child Basta to Shackleton about the required of the beta Ascension for the region. Two claws. Similar. Like her, is it able to carry files on piece cut design rotation, similar to lollipop clubs, Marco markers. Appointment time to use the
4-4 automatically generate a bad cough or figures presently. If you want to add a highest kind chips, you can tigers be used for masturbation data at notations. Yeah, as long as you have the peak spell, I think the eu's to annotate a text to. Amy type of data that had genomic ranges. I didn't have a data that it can be converted to be in a location. Chromosome name, I started and, or even just a small Peak side and you be able to use that began on Hall. Crystal
markers cheap speaker will consult with your preferred stock tractor, your actual signal, forestry or monk, i t. Fun to have one controller for all the markers are for. Each is two separate controllers. Rex, Rex Meneses. I understand if you have a monkey or otherwise, I think you prefer to be called great, to be able. Sometimes I see why you was an IGG off, all other sins. So there are several reasons for Falls. Antonio's, I GTA is that because you have a thoroughly as a prepared by
different species as you prepare for a specific antibody generator. Good background for you, it'll be our generator 5. I duplicate great designer with low complexity, so it's all good. You know, me, courage under this is a different position, so different I'll stay. They just do something different. From the other is that we should have one controller for all the keys to markers off of East Keystone Keystone temperature control. So is it recommended people are always such a thing
or two experiments yoyo repairs. Composer for all your experimental. Because the important role, some people think I'd be able to introduce some files. So you do not know if you are using deep and is also suggest you to use that. You can put There's a question about duplicates thing for this question. This is for the 3% instead. I think you should remove the duplicate race, otherwise, the signal can be best. So if you don't remove the duplicate Reese, Butler Funeral Home Bolivar High but it's just best.
Yet not sure whether that answer the questions. About the remove duplicate ZR2 to Singh's house. A new remote next to the first time is the next hip. Strain on us singing or background the ratio and then copies the compounds with the background. Do you want food remove Waits by yourself and they seem to be stupid. His research is not only come from a duplicate but also maybe it shows the true. A cheap single. So they have some Aldo to feed to feed the duplicator, has a
documentation of the team, call a person. I think they were just a mock, the duplicate resolve remove it is a good enough for you. Call people. Yes, like a muscle action. Max 2 has a way to acclimate weather. So that's why they asked me to work. Another bottle question law about child abuse upon a highlight in space original region. Have you remember to add line special position? So kind of Science by Sam script. So it says the design of the report scraped up to
generator the packs. All right, we are pretty much at the end of the session and perhaps there is one more question. So proud. How does chip dip chips, chips, Econo Econo, signs the nearest, my location shortest direction from Xbox One to be patient. If your side, is a 5K rise up, GNC auto in India in the file case. So, if you say that the nearest Direction promoters, ABC. So it looks like they too much. It gives your voice of flexibility and depends on your biological question. You should sit in. Yes.
All right, well this brings us to the conclusion of this session. Thank you all for grades presentations. Great questions is just said that a full of history and I want to make sure that they compare. This is so you might want to look. I just saw a paper so and the Funky Lillian genetics the computer so you might want to know the person who just want to say that if you can share that paper in the chat. Thanks everyone.
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