You submitted your comprehensive genome analysis job and you want to see how it's progressing and if it's finished, you want to look at your job results. How do you do that? Well, you could go into Workspaces and click on "My Jobs", or if you know the folder you put it in, which I never remember, you could click on "Home" and go to that exact folder or you could go down here to the "Jobs" monitor, double-click on that, and that will reload the page and you'll get directly to your present and past jobs. This is a great source of information, it'll show you your victories and occasionally your defeats as well. Now, notice this vertical green bar, it's totally blank, but if there's a job I want to see, I click on this row and notice that it populates the vertical green bar with possible downstream steps that I could do. If I had a problem with a job, I would click the "Report Issue" icon, but if I wanted to see, I would click on the "View" icon so let's click on that. This reloads the page to show all the information about this job that I submitted. Up at the top, you see the genome name and where it is in my workspace. This is the breadcrumb for this particular job. Up here, you can see some of the information about the job, the job ID number, when it started, when it completed, and how long it took to run. If I were to click on the parameters, it would tell me everything that I selected when I was at the interface and submitting this job. But what I really want to see, and what this video is devoted to, is the things that you get when you do this in Patric when you submit this job. I've already discussed the full genome report. It's one of my favorite documents in Patric, it shows you the assembly statistics, it shows you the annotation statistics if you've had any hits to virulence factors or antimicrobial resistance genes, where those genes are in a circular view of the entire genome, and it gives you a small tree that's based on a few genes to give you some indication of where your organism is in the great scheme of things. I encourage you to look at that particular file, but for this video, I just want to go over some of these higher-level folders that you see here. Now, annotated genome, because it ends in this.genome, I can't do it, I would have to download it and look at it. This is a genome type object JSON file that gives all the information about this particular annotation job and what was assigned to this genome. If you open it up, you'll scroll through it, it's gigantic and goes on. Well, it's not gigantic in size, but it just scrolls down and gives you information about every gene. It's a JSON, which is a JavaScript object view of the data. What it's showing you is data that this file is really for a computer to read. I'm a biologist. I don't read those things, but the computer scientists I work with, they do read it. I guess the importance of it depends upon where you're coming from, and we provide it there for you if you want to see it. You'll notice these two things, annotation and assembly. They both have this little checkered flag which is an indication that the job completed well, think of NASCAR or the one that they do in Europe, the name escapes me, when the race cars flash through, they do the checkered flag. We'll talk about those two things in a later tutorial. I'm going to skip this now. But the checkered flag is an indication that there are additional files. We don't know really what you want. We try to give you everything that you'll need and some things probably you don't need. But we want to be comprehensive in what we give you. You notice we have circos png and circos svg. The png is a portable network object. The svg is a scalable vector graph. These are both pictures, and we'll look at one, of this very large view of that circular view that we provided you with in the HTML that shows you the genes on the forward strand, the genes on the reverse strand, the RNA genes, the virulence factors, its antimicrobial resistance genes, GC scale and GC view. You can download it. The reason we give you these things is these are publication-quality figures that you can use, if you desire, within a publication. We want to give you something like that rather than forcing you to recreate it. Now I'm here, how do I get back? You notice that this is a hyperlink. I just click "Back" and it's going to take me back to where I was. We also give you a scaled vector graph of the codon tree that was generated, so you can download it, but we can view it. Remember from the report earlier, the genome you submitted is always this little red one. Let's go back. Codon trees, genesPerGenome.txt, if I click on that and click the "View" icon, that's going to show me within that tree that I just showed to you what the genome IDs, the genomes were and impact frequencies here for us just the genome IDs. How many total genes they had. This particular genome had this many genes. These were single copy and five of these were used to generate the tree. I emphasize this when we talked about that Genome Report. These trees are built on five genes. Five genes is not enough to, I think, do a publication or publish that data. I would encourage you to use our phylogenetic tree service and use more genes, 100, 500,000. Five genes is just to give you an indication, and we want it to run really fast, so you get this quickly. That's why we don't put more in there, but you should, and you should add in additional genomes. Let's go back. The.nex is a NEXUS format file that contains the genome tree. [NOISE] Things like Mr. Bay's and stuff can read this particular format. PgfamAlignment statistics, well, let's look at that. So we view that. This is showing me all the PGFams, which are the global families that we create at PATRIC. We generally start with global families because they'll be different genera within the tree. These are the statistics for those global families. But most importantly, it will tell us who was used and who wasn't used here. Used in analysis, and so they're different statistics that you might want to have with that. [NOISE] Then we have PGFams and genes included in the alignment text. We click on that and view it. That tells me what the identification number for that global protein family in PATRIC was. These are the individual gene identifiers for each of those genomes that were used in that and tells you if it used the protein or codons, which is the nucleotide for that.[NOISE] Then there's the Newick file. The Newick file is the information for the tree. We provide you with a view of what the tree looks like. But I like to open the Newick file in big tree. If I'm going to publish it, I like to manipulate it in just the way I want for a publication. This is a file that gives the instructions for building the tree. [NOISE] The subsystems color JSON file. This is once again a JSON formatted file, and it's used for rendering the colors in that subsystems pie chart. When we did the Circos PNG and SPG, we assign the different things that belong to the different subsystems, like protein coding genes, or metabolism genes were given a specific color. If you remember that from the Genome Report, this is just a descriptor of that. Then the tree ingroup, this is a file that contains the closely related genomes, building the ingroup of the phylogenetic tree in the comprehensive genome analysis service. You'll notice it uses the genome IDs and not the name of the tree. That's where we are with that. In the next video, we're going to talk about assembly and then the following one, the annotation. I hope you'll join us then. Thanks. Got my numbers a little screwed up. We're going to call this the third comprehensive genome analysis task, Part 2. We went through all the downloadable files that are provided after a comprehensive genome analysis job. I want you to go in to one of your jobs and open the following view in PATRIC, so you click on it and then click the "View" icon. Those are the jobs I want you to do, the Circos, the different flavors of that, the different codon tree files and the tree_ingroup.txt. Then just so you can see what a Newick file looks like, that's the file that gives the instructions for building the tree. Download it and then open it with some text editor. You could even open it in Word, but that would be a mess. But if you have something like text or something, do that. Take a look, get comfortable with these things. Just so you know, what you get with all the analysis services in PATRIC.
