Bulk RNA-Seq Analysis Demystified: Step-by-Step Tutorial Part 1

Welcome to the first part of our series on Bulk RNA-Seq Analysis! In this comprehensive tutorial series, we will delve into the intricacies of RNA-seq data analysis, covering every step of the pipeline. From Miniconda installation to advanced analysis techniques, we've got you covered.
In this first part, we focus on Miniconda installation and management, as well as the setup of essential packages within the Miniconda environment. Stay tuned for upcoming tutorials where we'll explore tools like FastQC, MultiQC, SortMeRNA, Trimmomatic, HISAT2, STAR, FeatureCounts, HTSeq, DESeq2, edgeR, GSEA, SRA Tool, and more!
#learning Innovatively with Me
Download the Miniconda installer for Linux:
wget repo.anaconda....
Run the installer script:
bash Miniconda3-latest-Linux-x86_64.sh
Initialize Miniconda:
source ~/.bashrc
Verify the installation:
conda --version
conda basic command
conda
Creating and Managing Environments:
conda env list: List all created environments.
conda create --name [env_name]: Create a new environment with the specified name.
conda activate [env_name]: Activate the specified environment.
conda deactivate: Deactivate the current environment.
conda env remove -n your_environment_name for this first go to your base environment and then remove the other
Managing Packages:
conda list: List all packages installed in the current environment.
conda install [package_name]: Install a package in the active environment.
conda update [package_name]: Update a package in the active environment.
conda remove [package_name]: Remove a package from the active environment.
conda list: List all packages installed in the current environment.
conda install -c conda-forge pakage_name -y
Searching Packages:
conda search [search_term]: Search for a package to see if it is available to conda install.
conda config --add channels [channel_name]: Add a channel where Conda will look for packages.
conda config --show channels: Show the list of channels.
conda config --remove channels CHANNEL_NAME
conda config --set channel_priority true
conda search -c CHANNEL_NAME PACKAGE_NAME
C channel
Exporting/Importing Environments:
conda env export forward angeled bracket environment.yml: Export the current environment to an environment.yml file.
conda env create -f environment.yml: Create an environment from an environment.yml file.
To search for packages on Anaconda Cloud, you can visit the following URL and use their search bar:
conda config --add channels conda-forge
conda config --add channels bioconda
Disclaimer:
The information provided in this tutorial is intended for educational and instructional purposes only. The tutorial creator and platform do not assume any liability for any errors, omissions, or inaccuracies in the content. It is essential to exercise caution and follow best practices when conducting experiments and data analysis in a laboratory setting.

[@AbdulManan-ob3xj]

Great work :)

[@burakkahveci4123]

Thanks

[@InamUllahKhan-z2m]