We will be using the unix terminal to run our analyses. so be sure you have access to one.
- Mac OS and any linux distribution will have a terminal already
- Mac OS: search for terminal in your spotlight search
- Windows users:
- Option 1: Download a unix subsystem (WSL) **recommended
- Option 2: Download MobaXterm
Note: It is required that you have some very basic knowledge on how to use the linux terminal as we will not go through basic unix commands in the workshop. Be sure you are okay with moving files, creating directories, and reading file content. For example: up until tutorial 2 from this tutorial. Here's another unix basics tutorial.
- Python3 is required
- conda can be useful to install cutadapt
During the workshop we will be using some known bioinformatics software to process our dataset:
- FastQC
- MultiQC
- CutAdapt - can be installed with pip or with conda
- Bowtie2
- Samtools
- IGV - Optional, if you want to visualize. Please install by following the website instructions.
To install the software please open your terminal and copy and paste the following commands inside the text boxes.
Most of the software we need is availble through the package manager.
sudo apt install fastqc
sudo apt install bowtie2
sudo apt install samtools
pip install multiqc
pip install cutadapt
First install Homebrew or any other package manager.
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
Then you can use brew to install the packages.
brew install fastqc
brew install bowtie2
brew install samtools
pip install multiqc
pip install cutadapt
To check that the program works, you can check if the help message gets printed:
fastqc --help
bowtie2 --help
samtools --help
multiqc --help
cutadapt --help
Some problems may arise while installing software. Be patient and read the error message, it could be due to some dependecies missing. Googling the error message is a good first attempt to solve it.