Fly-CURE: Shell Genomics, Data Wrangling, and SNP Analyses: Glossary

The shell gives you the ability to work more efficiently by using keyboard commands rather than a GUI.

Everything you need to utilize in class is housed in our JupyterLab app.

Login in to CyVerse and launch our class app everyday before class.

The shell gives you the ability to work more efficiently by using keyboard commands rather than a GUI.

Useful commands for navigating your file system include: ls, pwd, and cd.

Most commands take options (flags) which begin with a -.

Tab completion can reduce errors from mistyping and make work more efficient in the shell.

The /, ~, and .. characters represent important navigational shortcuts.

Hidden files and directories start with . and can be viewed using ls -a.

Relative paths specify a location starting from the current location, while absolute paths specify a location from the root of the file system.

You can view file contents using less, cat, head or tail.

The commands cp, mv, and mkdir are useful for manipulating existing files and creating new directories.

You can view file permissions using ls -l and change permissions using chmod.

The history command and the up arrow on your keyboard can be used to repeat recently used commands.

grep is a powerful search tool with many options for customization.

>, >>, and | are different ways of redirecting output.

command > file redirects a command’s output to a file.

command >> file redirects a command’s output to a file without overwriting the existing contents of the file.

command_1 | command_2 redirects the output of the first command as input to the second command.

for loops are used for iteration.

basename gets rid of repetitive parts of names.

Scripts are a collection of commands executed together.

Transferring information to and from virtual and local computers.

Spend the time to organize your file system when you start a new project. Your future self will thank you!

Always save a write-protected copy of your raw data.

These lessons help you understand NGS sequencing methods and how .fastq files are generated

It’s important to record and understand your experiment’s metadata.

Quality encodings vary across sequencing platforms.

for loops let you perform the same set of operations on multiple files with a single command.

The options you set for the command-line tools you use are important!

Data cleaning is an essential step in a genomics workflow.

Bioinformatic command line tools are collections of commands that can be used to carry out bioinformatic analyses.

To use most powerful bioinformatic tools, you’ll need to use the command line.

There are many different file formats for storing genomics data. It’s important to understand what type of information is contained in each file, and how it was derived.

We can combine multiple commands into a shell script to automate a workflow.

Use echo statements within your scripts to get an automated progress update.

This is an authentic hypothesis-driven research project spanning multiple semesters and institutions.

for loops let you perform the same set of operations on multiple files with a single command.

FastQC enables us to validate the continued use of the sequencing data.

The options you set for the command-line tools you use are important!

Data cleaning is an essential step in a genomics workflow.

Bioinformatic command line tools are collections of commands that can be used to carry out bioinformatic analyses.

To use most powerful bioinformatic tools, you’ll need to use the command line.

There are many different file formats for storing genomics data. It’s important to understand what type of information is contained in each file, and how it was derived.

Bioinformatic command line tools are collections of commands that can be used to carry out bioinformatic analyses.

To use most powerful bioinformatic tools, you’ll need to use the command line.

There are many different file formats for storing genomics data. It’s important to understand what type of information is contained in each file, and how it was derived.

Bioinformatic command line tools are collections of commands that can be used to carry out bioinformatic analyses.

To use most powerful bioinformatic tools, you’ll need to use the command line.

There are many different file formats for storing genomics data. It’s important to understand what type of information is contained in each file, and how it was derived.

Bioinformatic command line tools are collections of commands that can be used to carry out bioinformatic analyses.

To use most powerful bioinformatic tools, you’ll need to use the command line.

R script used to generate useable list of unique SNPs for each mutant.

End of the bioinformatics pipeline.