Bulk PE RNAseq data analysis, GNU/Linux-Ubuntu

Before You Start

Ensure your system is up-to-date and has necessary dependencies installed.

1. Update your package index: sudo apt-get update and sudo apt update serve the same purpose: they update the local package index. But apt update is the recommended command to use for most users due to its simpler syntax and user-friendly output.
2. Install build-essential: you can use this command: sudo apt install build-essential The build-essential package typically includes various tools and libraries needed for building software from source code, such as compilers and development libraries.
3. If you encounter missing dependencies, use: sudo apt-get install --fix-missing This command will try to fix any missing dependencies that may prevent packages from being installed properly. It's useful if you encounter errors related to missing dependencies during the installation process.
4. Use pwd to check your current location. You can use wget to download the required tools.

Requirements

Download the following tools and genomes:

1. FASTQC v0.11.9

• Download link: FASTQC v0.11.9

2. TRIMMOMATIC 0.39

• Download link: TRIMMOMATIC 0.39

3. SAMTOOLS-1.18

• Download link: SAMTOOLS-1.18

4. HISAT2 v2-2.2.1

• Download link: HISAT2 v2-2.2.1
• Get the genome: HISAT2 Genome # Don't forget to select your model's genome.

5. featureCounts

• Download link: featureCounts
• Get the genome: featureCounts Genome

Creating a Shell Script

Follow these steps to create and execute a shell script:

1. Open your terminal.
2. Create a shell script file named "yourshfile.sh" using the text editor "gedit":

gedit yourshfile.sh 

3. Write your shell script code inside the editor.
4. Save the file and close the editor.
5. In the terminal, make the script executable:

chmod +x ./yourshfile.sh

6. Now, you can run the script using:

./yourshfile.sh