Setting Up the RNA-Seq Environment with Miniconda

This guide explains how to install Miniconda, set up a conda environment, and install essential tools for RNA-Seq analysis.

Step 1: Install Miniconda

Download the installer from the Miniconda website

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

Step 2: Run the installer:

bash Miniconda3-latest-Linux-x86_64.sh

Press Enter to continue and view the license agreement.

Use the Up and Down cursor keys to browse through the agreement.

When prompted to accept the license terms, type yes to proceed.

Press Enter to continue and start the installation.

Step 3: Activate Miniconda

source ~/miniconda3/bin/activate

Step 4: Verify the installation

conda --version

Step 5: Initialize Conda

conda init

Step 6: Create a Conda Environment

conda create --name rnaseq_PPL

Step 7: Activate the environment

conda activate rnaseq_PPL

Step 8: Install Rna-Seq Tools (FastQC,Trimmomatic, Samtools, HISAT2, Stringtie)

Install the required tools into your conda environment

Install FastQC

conda install bioconda::fastqc

For each installation, type y when prompted to proceed.

Install Trimmomatic

conda install bioconda::trimmomatic

For each installation, type y when prompted to proceed.

Install SAMtools

conda install bioconda/label/cf201901::samtools

For each installation, type y when prompted to proceed.

Install HISAT2

conda install bioconda::hisat2

For each installation, type y when prompted to proceed.

Install StringTie

conda install bioconda::stringtie

For each installation, type y when prompted to proceed.

Step 9: Verify Installation

Check the versions of installed tools to ensure everything is set up correctly

FastQC

fastqc --version

Trimmomatic

trimmomatic -version

SAMtools

samtools --version

HISAT2

hisat2 --version

StringTie

stringtie --version

With all tools installed, you're ready to proceed with your RNA-Seq analysis.