Everyone, in the last video I showed you how to submit reads to the comprehensive genome analysis service. Today, we're going to talk about submitting contigs. So let's go into services. Click the down arrow, and then click here on comprehensive genome analysis. This opens up the landing page to the tool. You can submit reads as we've talked about before, or assembled contigs. This is one of the places in PATRIC that you can use assembled contigs and submit them for analysis. You notice that when it's to read, It's a pretty complicated interface and when it's assembled contig, it's pretty easy. Now if you know what your contigs are called, you could just start typing and PATRIC is going to try to find something that matches whatever text you put in there. Also you could click on this down arrow and it'll show me all the contigs files that I've generated in PATRIC, from the most recent backwards. Or you may want to upload some data. So you would click on this folder icon. Here we have the upload button. This is showing me that it's my workspace in my computer and I could go in and upload it into a specific folder if I wanted to. Then I would click the upload monitor to do that which would right away say, because it knows, that we're looking for contigs. So you know this has got the upload typing contigs here. If you wanted to have wrote something differently, you could of course, but you'd have to do it outside this part of the tool because it's looking specifically for contigs. It's going to look for files that end in FA, fast day or FNA. That's the signal, that's the type of ending that these files have to have to tell the servers that they are indeed contig files. I could click "Select File", which opens a dialog box with my computer where I could find files to upload. But you know what, I don't want to do that because I have some files for us to look at. So up here where it says workspaces. This is my private workspace, but we want to click the down arrow and go to public workspaces because I have prepared some great data for you. This is what all the public workspaces that are shared with me, yours may look a little bit different. Let's go down and where we see PATRIC workshop, let's click on the globe here. Then this shows me within that particular workspace, all the different folders with data that are in there. So let's click "Assembly". I want you to click on this folder, the "SRR779651". So we'll click on that and it shows me that I have some files here. This is the symbol for contigs. So let's click on that. Then we click "Okay". Now you can see that file is here. Now we have to put in the parameters for the annotation job. This is going to take over the annotation of contig, but we need to provide it with some information. What's the taxonomy of this organism? Well, you don't know, but I do know that it's Buchnera. I'm going to start writing it here, Buchnera, and then it gives me a genus. So I put that in and notice that it auto-fill the taxonomy ID. Then I need a identifier for it. So I'm going to give it this number that tells me it came from the SRA, and then I'm going to give it a date. So I just have been doing that a lot lately, dating everything so I can see exactly when I did run it. What if you don't know what it is. You don't have to fill in the taxonomy or you could use the taxonomic classification service to figure out what organism it is. You want to try to get to genus if you can because PATRIC gets you two flavors of protein families. The global families which cross the genus barrier and boundary, and the local families which are genus specific. So if you want to do a really fine tune comprehensive analysis within the genus, you need that to get this particular flavor. Genetic code. We have offered three here. We're going to pick bacteria and then the output folder. So you can click on what you did most recently and find that, or you can create a folder for your analysis yourself. I'm going to see if I can find my comprehensive. Look, it tells me comprehensive genome analysis. I'm going to click on that folder and look here. It's blue now and that means I can submit the job. I've got the contig, I've got the taxonomy, I've given it a name, a genetic code, a folder, it's all ready to go. So let's click "Submit". Then you can see there's a message here that's saying the job has been submitted and its been cue. You can monitor its progress on the jobs monitor down here at the bottom of the page. In the next video, we're going to show the files that come with the job once it's completed. Thanks for watching. So you probably got a little tired after the last assignment where you had to submit all those jobs. So this one's going to be a little bit easier, but we're now already at our second task for the comprehensive genome analysis. Here's the first thing you have to do. The folder that you've created and Task 1, you'll need to copy over a contig file. Now remember, you can create sub-folders within there to keep it as neat and clean as you desire. Not as possible, but as you wish because remember it's your workspace, you make the decisions, not me. One thing that's going to be important is you need to make sure that those files are tagged as a contig file, and then you're going to need to submit the job. So where are those files? You go into workspaces, click on "Public Workspaces". This will take you to the public workspace folder. You scroll down until you find MOOC PATRIC Course and double-click on the globe. That'll open up. You'll see three folders there. Click on "Comprehensive Genome Analysis". Actually I keep adding on, so you'll see more and more as time goes on. So you click on comprehensive genome analysis. This will open up and there will be three folder box there. Click on "Contigs", and there's the one you want. Still need to click on that. This is just a hint to help you. Because if you didn't pay close attention back in the assembly tutorial, in the annotation tutorials earlier before we did comprehensive genome analysis. We talked about changing how these different things are tagged. So you're going to need to go there and do it. Good luck, I know you can do it. Then you only just need to submit the job and you're on your way. See you next time.
