In this instructional video, we're going to go over the different types of read files that PATRIC allows you to use when you submit them to the assembly service job. To find the assembly service landing page, you click on "Services" and then "Assembly". PATRIC accepts three types of files: paired reads, single reads, and accession numbers from the Sequence Read Archive. Let's talk a little bit about paired reads. If you've recently uploaded data into PATRIC, you could click on this down arrow here and it would show you the most recently loaded data that you put in. That would be pretty easy to find that file that way. However, if you loaded your reads a long time ago, you may remember what you called them and you can start typing the name, what you recall and the autofill function in PATRIC will try to find files with text that matches what you typed and you can find it that way. Another way is to go directly to the workspace and find data that you loaded previously. We're actually going to use this because I have uploaded some data for you. This is my workspace, but click on this down arrow here and then click on "Public Workspaces". This will reload this data to show all the public workspaces that you have access to. Because I'm logged in, you're seeing ones that I have access to. They won't be the same as yours, but we each should have this workspace, which is called PATRIC Workshop. Click on this little globe icon here, and that shows all the folders within PATRIC workspaces. Click on the folder icon for Assembly, and that shows all the data that's there. Now, for today's example, we're going to use this data that came from the Sequence Read Archive, this 3584989_data folder. Click on that. We can only click on one at a time, let's click on the first read and then click ''Okay''. Now, we need to get the mate to it, so we click on the folder icon, Workspaces, click on ''Public Workspace''. Scroll down until you see PATRIC Workshop, click on the globe, click on the Assembly folder, click on the SRR3584989_data folder, and click on the second pair of that pair again. We have our paired-end reads here. It's a good time to look and make sure that they match, that you've got the numbers lined up correctly. You notice that there's an Advanced button here at the bottom of the box. Clicking on that shows us three different boxes. One for interleaved, one for mate pairs, and one for platformed. What is interleaved? Interleaved files occur when the R1 and R2 reads are combined in one file so that for each read pair, the R1 read in the file comes immediately before the R2 read, followed by the R1 read for the next pair and so on. This actually doesn't happen very often, that's why the default is set for false. Thus, if you do have that, you can click on this down arrow and click for true. Mate-paired is something that also doesn't happen very often. It's a specific type of library that allows you to have your pairs much farther apart. This can be more informative than the standard paradigm protocol and they're generally bigger. But like I said, it's very rare. If you do have this mate-paired library preparation, you would click here and do true. The last is infer platform. You notice that the default says infer platform, but if I click the down arrow here, you can select Illumina or Ion Torrent. Those are the only two sequencing platforms we know of right now that have paired-end reads, so I'm just going to leave that at infer platform. This is the information I want tagged to my reads and I need to remove these reads into my selected library box. To do that, I click on this little arrow in the upper-right corner of the paired read library box, and it moves it there, and I can look by mousing over the eye or the information icon that it says there's a paired library. It's instructing PATRIC to infer the platform, and it's showing the two different reads and where they came from. Single read library. Now, you can combine paired and single read together. You could combine a number of paired read libraries. Imagine, often with sequencers, often the technician will load or repeats of the same sampling, a number of lanes so in case one fails, so you can have multiple backups. You could combine all of those to get a greater coverage of your data. But another thing you can do if you have PacBio and Illumina, people often do this to get a better assembly with deeper coverage, you can combine those by having your Illumina reads come in through the paired read and your PacBio reads come in through the single read. You do the same thing to load that by clicking on the file and then uploading it through the workspace. If you had a file there and you click on "Advance", and let's look at platform, you'll notice that you could have single read Illumina, single read Ion Torrent, or a long read PacBio or Nanopore that you could add. PATRIC also allows you to submit data from the Sequence Read Archive. Let's say you know an accession number, you have one that you found that you want to assemble the data for, often because it's sometimes a problem to submit data to GenBank if you have an assembly or an annotation, a lot of people are putting the data directly into the Sequence Read Archive, and so the only way you can get access to that data to compare it to your own is by assembling and annotating it independently. You can use this function to be able to load that data into an assembler. You could either write in the number or you could cut and paste it from the Sequence Read Archive. Let's say I have a run accession number, when I click this arrow to add it to my selected libraries box, you notice that there was a brief message that said it was validating it to prove that it was a good accession number. If I were to submit this job now, it would be combining these two things. Anything that's in the selected library box will be combined together. But no, I made a terrible mistake. These things don't belonged together. You can remove it very easily by clicking on this button here. In the next video, we'll talk about the parameters box and submitting the assembly job. There's your second assignment. Remember when you created a folder and you uploaded those MOOC reads in them? You're going to have to find them now, and you're going to need to upload them in the app, and you're going to need to move those reads into the selected library box within the service. Good luck. Let me know if you have any problems.
