Command-line Based Practical RNA-Seq Data Analysis With Linux & R


About This Course

Why Learning RNA-Seq Data Analysis is Important for Your Career?

Learning the underlying concepts of RNA-Seq Data Analysis and the practical applications of RNA-Seq can be beneficial for you and your research career. RNA-Seq is an exciting and in-demand next-generation sequencing (NGS) method used for identifying genes and pathways underlying particular diseases or conditions. Therefore, you can take any RNA-Seq data from any public repository and find out which biomarkers are being expressed differentially in two different conditions. These biomarkers can then be useful for therapeutics for that particular disease or condition. 

How Will this Course Benefit You?

One of the major benefits that you will get from this course is that it is based on Linux/R analysis, that means even if you lack any prior knowledge of Linux or R, DO NOT WORRY! You will first go through a few lectures of Linux that are required for you to get started with RNA-Seq Data Analysis and by the end of this course, you will have a greater understanding of Linux and R for RNA-Seq Data Analysis. The entire course is based on Linux command-line tools, and you don’t require any prior knowledge, you will learn every little command required for RNA-Seq data analysis in this course.

RNA-Seq is highly in-demand and nearly every research lab or job prospect requires you to know RNA-Seq and NGS pipelines and data analysis techniques, hence making this course the perfect fit for the in-demand industrial requirement, that can and will be helpful for your resume, if you just put down on your resume “Expert in RNA-Seq Data Analysis”. Learning RNA-Seq Data Analysis has become an increasingly valuable skill, especially for those who are still in Bachelors, Masters or even Doctoral degrees.

Get yourself enrolled in this in-demand course and learn industrial level RNA-seq workflow and analysis, leading to skills in discovering differentially expressed genes and biological processes which might be important for your condition of interest!

What Will You Learn?

You should watch the introductory video, it’s 45+ minutes long and it is free.

In simple terms:

  • What is RNA-Seq and how the analysis is performed
  • Command-line tools required for RNA-Seq Data Analysis
  • In-depth theoretical and practical knowledge of RNA-Seq Data Analysis
  • DESEQ2, edgeR and Ballgown (R-language packages) for Differential Gene Expression

The course starts from the very basics of Next Generation Sequencing and RNA-Seq, covering both theoretical and practical aspects of each topic of the entire RNA-Seq data analysis pipeline. 

  • First you will learn what RNA-Seq is, and how and what kind of raw data is produced in RNA sequencing.
  • Each and every step of RNA-Seq will be theoretically introduced to you before diving into the detailed theoretical and practical aspects of each topic. 
  • You will be taught how to retrieve raw RNA-Seq data (EMBL-ENA, GEO, TCGA, ArrayExpress or others) and how to prepare it for RNA-Seq data analysis.
  • You will then be introduced to Linux for Bioinformatics lectures which will guide you about the basics of Linux and what you need to know before proceeding with the actual RNA-Seq data analysis.
  • You will then learn what is quality control and what is the need to do it and how you can preprocess your raw data with quality control (FASTP, FASTQC, Trimmomatic, Cutadapt).
  • You will then learn the difference between reference genome based assembly and alignment of the raw reads and de novo assembly. You will then learn command-line tools for alignment and mapping (TOPHAT2, BOWTIE2, HISAT2, STAR)
  • You will also learn how to inspect your results of the alignment, how to interpret them and what are the factors of a good alignment.
  • One of the most important aspects of RNA-Seq data analysis will also be taught which is the quantification of raw reads for each gene using StringTie.
  • Finally, you will learn how to use DESeq2, edgeR & Ballgown to identify differentially expressed genes using the count data.
  • Visualization of the results with heatmaps and volcano plots will be performed and the significant differentially expressed genes will be identified and saved, ending with Functional Enrichment Analysis Gene Ontology and Pathway Analysis.

How Will You Learn?

The entire course is pre-recorded and online, that means you can learn at your own pace and watch the lectures as many times as you want and complete the course whenever you have the time! So, all you have to do is click “Add to Cart” on this page, create an account and purchase the course. Afterwards, your account will automatically be activated and you will see all the course content on your learning dashboard, where you can access each lecture video along with its transcript and notes. 

Is it for Beginners?

Yes! This Command-line Based Practical RNA-Seq Data Analysis With Linux & R is absolute beginners who have no prior experience in Linux, R or even RNA-Seq. That means, you can get started right away and you will be taught everything you need during the course. Just like the below mentioned learners who had no prior experience in RNA-Seq analysis!


Shehroze Tariq, a student at the University of Pisa, Italy contacted BioCode a few weeks ago to enquire about our courses and how they could benefit him with this research on plant biotechnology-related research on which he was stuck for a quite a while. He had been trying to learn RNA-Seq analysis from YouTube and other free sources but all his efforts were not fruitful as he failed to make any progress in his research, since the topics covered on YouTube were not in-depth and he lacked proper understanding of RNA-Seq data analysis or any of its sub-processes. He wanted to quickly learn RNA-Seq data analysis that could help him complete his research before the deadline and he wanted a course that could cover all the basics of RNA-Seq, all the way to differential gene expression analysis. He enrolled in the BioCode course and was able to learn RNA-Seq Data Analysis and fulfill his research goals.

Few months back, I was looking for some good bioinformatics platform to get a training in advanced level bioinformatics techniques. After thorough search, I came across BioCode 60 Days Internship plan. Without given a second thought, I signed up for that as whatever I wanted to learn was included in that internship plan. I completed that internship plan and I am extremely satisfied with the contents, video lectures and support /guidance which I got from time to time from the staff. I would highly recommend if someone wants to get advanced level bioinformatics training, BioCode is the place to start with. I myself now planning to start another training from this platform soon.

Thanks BioCode team for this fantastic learning.

Jamshed *******, from Pakistan

I started the internship on Functional bioinformatics by BioCode and it was, without a doubt, the best online activity on this subject that I attended so far. As a beginner in this field, I will totally recommend it to anyone with or without prior knowledge of bioinformatics. Besides that, their support team is one of the best.

Mushhood Ur Rehman, from PHFMC

I have been taking BioCode lectures for a few months now and I think it is the best platform to start with understanding the basics to the complexity of Bioinformatics and Computational biology. I highly regard the BioCode team as they are very cooperative and exceptionally helping people and always try to make things easy for you.

Faiza Munir, from Pakistan

BioCode have helped me a lot to be an international researcher.

Thank you for the opportunity, time and dedication at any time for 3 months!

Ergi Hoxha, from Albania, Faculty of Natural Sciences

Thank you for all your help. Your service was excellent and very fast. Many thanks for you kind and efficient service. I have already and will definitely continue to recommend your services to others in the future.

Sajjad Hussain, Harbin Medical University, China

I was surprised and amused by the content and the speaker. They taught from the very basic concept and slowly building an advanced level. Happy to be a part of the BioCode platform.

Muhammad Faizan, Pakistan

 I am currently enrolled in one of the workshops of BioCode and I am enjoying this course a lot. Although, I have no knowledge about proteins and bioinformatics I am learning a lot because the way it is explained is very good. On the other hand, I really appreciate the communication I have been having with the staff members. Although this is a virtual communication it is easy to notice that they are very supportive, respectful and collaborative, so that I am very happy of this choice. I am going to follow another course here and I suggest this to anyone interested to learn more and want to gain very good skills in several issues related to bioinformatics.

Inva Kociaj, University of Tirana

Is it Project Based?

Yes, the course is project based. That means the instructor takes a raw data set and performs the entire analysis on it which you can follow step-by-step. You will also be given a project by the instructor with proper guidelines, it will be available in your dashboard.

Is Raw Data Included and What Dataset is Used?

Yes, a raw data set is included in the course which you can easily access. We will be using this dataset in the course:

Is It An In-Depth Theoretical and Practical Course?

Yes, everything is covered in-depth, each lecture topic duration ranges from 20-50 minutes, therefore, we have covered everything that is required for you to do end-to-end RNA-Seq data analysis.

I don’t know anything about Linux/R?

That’s not an issue, you will learn the required topics of Linux and R in this course. 

How Will DEGs be Identified?

We will be using 3 different R packages Ballgown, edgeR, DeSeq2. You only need to use one, we will demonstrate 3 just to make sure you have an understanding of how to use multiple packages. 

Course Author 

Waqar Hanif is a Bioinformatician with extensive knowledge and experience in programming languages such as Python, R, Linux along with C/C++/JAVA. He has developed multiple Bioinformatics tools, some of which have been published (while some are under review) link 1, link 2. He has authored a book on RNA-Seq Data Analysis which you can find here. He is the founder and CEO of BioCode, leveraging his experience to create a better platform for learners from all around the world, where they can learn Bioinformatics, no matter to which field they belong to. 

No Prior Knowledge Required in RNA-Sequencing

Our course makes sure that you learn every little thing about the theoretical RNA-Seq analysis before you start making progress in the practical RNA-Seq analysis which will then feel as easy as 1, 2, 3. 

Guarantee that Matters!

Your Expertise in RNA-Seq is Guaranteed or You Get a Refund. No Conditions Attached!*

We guarantee that taking this course will not only help you in the short term such as completing your project that you are stuck in, but also greatly benefit you in executing RNA-Seq pipelines easily so that you can publish research that matters. 

Students are taught each topic in detail with prime focus on both theoretical and practical aspects of building an in-depth understanding of RNA-Seq data analysis pipelines. Our aim is not to teach you how to do RNA-Seq analysis, our aim is to make sure you know exactly how RNA-Seq data analysis is performed so that even if you encounter errors, you understand what they mean and how to fix such errors. 

The Challenge

We understand that you need to learn RNA-Seq Data Analysis and you have tried online tutorials from all around the web, but you never understood anything. RNA-Seq is actually hard, we agree with you. But, not when it is taught properly!

The Solution

BioCode brings the exact kind of solution for you that you need, a proper end-to-end in-depth RNA-Seq Data Analysis course that you will learn at your own pace at any given time of the day and complete it whenever you have the time. A project-based learning course where you learn each and everything about RNA-Seq Data Analysis in step-by-step procedure through Linux and R based methodologies. 

The Results

By the end of this course, you will be able to do RNA-Seq Data Analysis, end-to-end. You will have a better understanding of Linux and R. You will know how to identify differentially expressed genes in two different conditions, you will know how raw data is sourced. You will also know how to preprocess the raw data and exactly which aligner should be the best for your data and many more things!

Learning Objectives

Introduction to RNA-Seq, NGS
In-depth Knowledge of R & Linux
Command-line tools for RNA-Seq
Quality Control and Trimming
Mapping & Evaluation of Alignment
Discovering DEGs with DESeq2, edgeR and Ballgown
Functional Analysis with Gene Ontology & KEGG Pathways


  • No Prior Knowledge of R or Linux Required
  • No Prior Knowledge of RNA-Seq Required

Target Audience

  • The target audience for this course are biologists, beginners in Bioinformatics with no or little experience in R, Linux or RNA-Seq
  • People who need to discover differential gene expressions in their dataset
  • People who need to complete their RNA-Seq research


57 Lessons7h

In-Depth Introduction to RNA-Seq

In-depth Introduction to RNA-Seq Data Analysis, Linux Computing and R44:08
Introduction to Linux for Bioinformatics22:32
Introduction to ArrayExpress – Getting Started With MicroArray Analysis9:56

Genomic Databases for Raw Data

File Formats

Introduction to Linux for RNA-Seq

RNA-Seq Data Analysis Pipeline (Theoretical & Practical)


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30% off
All Levels
Duration 7 hours
57 lectures

Material Includes

  • Become a Certified RNA-Dataset Analyst
  • Step-by-step video lectures
  • Subtitles (English)
  • Learn any time, any where!
  • Transcription
  • Notes
  • BioPresentations
  • Exercises
  • MCQs
  • Certificate

Enrolment validity: 365 days

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