Hello! Today we'll be going through some hands-on activities to help you get familiar with how many bioinformatics tasks can be done directly from the command line.

The first thing you should do if you haven't done so is connect to the ConGen server. We'll be working exclusively in the RStudio browser interface that you should be familiar with by now, but if you have questions or problems at any point please feel free to ask! Just in case, here's an annotated picture of roughly what you should be seeing right now. If you are seeing something drastically different or something that you don't understand, let us know.

Figure 1.1: The RStudio interface for running commands and browsing files.

Most of our work will be done as bash commands typed in the Terminal provided by RStudio. Throughout this walkthrough, commands will be presented as follows:

this is an example command

Following each command will be a table that goes through and explains each part of the command explicitly:

The goal of providing these tables is to break-down some of the 'black box' that command line tools can sometimes feel like. Hopefully this is helpful. If not, feel free to skip over these tables when you see them!

Commands that you should run will have a green background. We will also provide some commands that are beneficial to see, but do not necessarily need to be run using a red background, like so:

this is an example command that won't be run

Additionally, one of the most important and often overlooked parts of bioinformatics analyses is to simply look at ones data. There will be several points where we stop to look at the output of a given program or command. When we do, a snippet of the output will be presented in the walkthrough as follows:

Here is some made up output.
Looking at your data is very important!
You can catch problems before you use the data in later analyses.

Today we'll be doing some basic bioinformatics tasks from the command line. We'll get to the specifics of the data later, but for now please download the project template we've provided on github.

First, make sure you're in your home directory. If you're not, or you're not sure if you are, run the command:

cd ~

Next, download the project repository using git:

git clone https://github.com/gwct/congen-bioinformatics.git

Git is very powerful software for sharing your projects and used commonly to share code and data from scientific papers, but we won't talk about it much today other than using the clone command to download the project. You don't need a github account to clone a repository, but you do need git installed on your computer to do so.

After the clone command completes, you should now have a folder in your home directory called congen-bioinformatics. Make sure it's there with ls:

ls

And next change into that directory:

cd congen-bioinformatics

Using this project template data, we'll be performing the following tasks today:

1. Talking about project organization, common commands, and text editors and work setups.
2. Introducing common bioinformatics file formats.
3. Using the command line to do a basic analysis of structural variation in a sample of 32 Rhesus macaques and of SNPs in 35 gray wolves.
4. Time permitting, briefly touch on some next steps in developing more advanced bioinformatics skills

Now, let's move on to Project Organization