Benoukraf Lab

💻 Installation Guide: FastQC, IGV, and RStudio

Please follow these steps to install the required tools for the RNA-seq workshop.

🔹 1. FastQC

✅ Website: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

  • Windows:
    1. Download the Windows ZIP file.
    2. Unzip the folder to a location like C:\Program Files\FastQC.
    3. Inside the folder, right-click on fastqc.exe → Properties → check Unblock (if present).
    4. Add the folder to your PATH (optional but recommended):
      • Search Environment Variables → Edit environment variables → add the FastQC folder path to the PATH variable.
    5. To test: Open cmd → type fastqc --help.
  • Mac:
    1. Download the Mac DMG or ZIP file.
    2. Unzip or install into /Applications/FastQC or a folder you prefer.
    3. To run from Terminal:
      • chmod +x fastqc (inside the folder)
      • Run using ./fastqc or add the folder to your PATH.
    4. To test: Open Terminal → type fastqc --help.

🔹 2. IGV (Integrative Genomics Viewer)

✅ Website: https://software.broadinstitute.org/software/igv/

  • Windows / Mac:
    1. Download the IGV for Java 11 appropriate for your system.
    2. Install or unzip the package.
    3. Double-click the igv.bat (Windows) or igv.sh / igv.app (Mac) to launch.
    4. Make sure Java 11 or newer is installed. If not, install from Adoptium or Oracle Java.

🔹 3. RStudio

✅ Website: https://posit.co/download/rstudio-desktop/