 So this presentation is just to introduce the group work, just a bit of an overview of the different project. So you know what to expect. So there are two projects that you can choose from maybe a third depends a little bit on your preference, but I'll ask around later on. So we have, I started with project three, because that's convenient. So project three would be short read RNA sequencing of mouse samples. So that data set comes from a very big publication, I think in one of the high end journals, I think I thought was nature. And it has some very nice are native data set relatively straightforward. And the aim here is to compare. I said to, to both I to two different aligners so you will learn more about aligners tomorrow. But the idea is to generate two different alignment and compare the two and see what kind of differences you find, for example in the in the alignment files. But of course first you would need to do the quality control and everything. So that's something you can already start with today, and tomorrow afternoon. Project one is short read RNA sequencing of Arab of Staliana. I don't know why I have this animation like this but So that's another project. It's very similar to the mouse project also there you will compare Hi said to to both I to main difference between the two is that the Arab of Staliana genome is, I think it's about 300 mega base pairs or so 0.3 gigabase pairs well the mouse genome is I think about three gigabase pairs. So the Arab of Staliana genome is about 10 times smaller compared to the mouse genome which means that you can use the whole data set for Arab of Staliana and only use a subset of the data set for for mouse doesn't really matter for both of them. The concept is clear that you need to compare these these two aligners. So, what you'll get. You can read all about that in the in the book work page is you get the sequence data, you need to download that sequence data and that because data you are asked to go through all the steps that we will perform in the course during the exercises so you need to do quality control and trimming. Later on you will of course also do alignment, for example on the E. coli data set and visualization, and you're also expect to do that with real data so the Arab of Staliana mouse data. So you're starting a bit on how far you will get. You might also do some counting as my gene expression so this RNA seek data and usually what you're why you are doing RNA sequencing data is because you're interested in gene expression. So if you count the number of alignment per gene, you get an idea of the expression of a gene, you are, you can compare the, for example, the two aligners and how that has an effect on the count table which you will, which you can later do as my gene expression, for example. So three important things I wanted to mention here. So, do not only perform the calculations but also try to get an idea of what you are doing and what the outputs are always check the outputs, do you get you get the expected result for example, you will learn more about file types during the course obviously so you can put that into practice, be reproducible, meaning try to follow these five table rules to at least have some reproducible scripts with the numbering and everything. And last but not least in the afternoon of day three, all groups so we have five groups of five people will give a 10 minute presentation. So, it is always a bit of a challenge. So I'm doing this now for the third or the fourth time it's always, I think it's always super nice because people really go from let's say zero really beginners to actually performing a night analysis and this who does what within a group and usually that goes quite easy and sometimes it's a it's a bit. Well it's a bit challenging depending a little bit on, you know, type of people who are in a group who want to do what and everything. So there, there are multiple ways you can do that but I would suggest. I think that's quite important, I think, is that at least the data you're working with so the reach you're going to download are in one directory you have a shared directory I will show that later on where that is. You have a share directory and please put your reads in there so you do not download, not everybody downloads. You can read in their home directory for example because otherwise it becomes full quite quickly. So start from the same reads, download them only once for the group. Other than that, you can either say okay, somebody is going to do, for example, going to focus on the alignment one on the quality control and one on something else or you can say okay we're going to kind of work individually. Somebody is going to do everything and at some point, or during the process we're going to communicate how things are going and you're going to help each other out. I think the latter one is the easiest way so that you do everything individually, but you ask your peers if things are not clear to you, for example. This is a typical example of a reverse platform where you teach each other stuff. Of course, I'll be around. I'll be visiting the breakout rooms very often, but don't worry about that. And if you doubt about anything or if you get frustrated or whatever, just let me know and I'll help you out.