Hands-on Practical RNA-Seq Data Analysis With Galaxy


About This Course

  • RNA-Seq is an exciting and in-demand next-generation sequencing (NGS) method used for identifying genes and pathways underlying particular diseases or conditions.

  • As high-throughput sequencing becomes more affordable and accessible to a wider community of researchers, the knowledge to analyze this data is becoming 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!

  • The course starts from the very basics of Next Generation Sequencing, the basics of sequencing and how the raw data is produced, then a detailed overall overview is given of the RNA-Seq workflow with an emphasis on differential expression (DE) analysis.

  • The course further covers; how to prepare data for RNA-seq analysis, do quality control and trimming, process the data for mapping against the reference genome, leading to quantification of raw reads for each gene, assess the quality of the count data, and identify outliers and detect major sources of variation in the data.

  • Finally, you will learn how to use DESeq2 to model the reads count data using a negative binomial model and test for differentially expressed genes. 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 Gene Ontology and Pathway Analysis.

Introduction to RNA-Seq Theory & Workflow

In this chapter we explore what is NGS, RNA-Seq and what can do with RNA-Seq data and why it is exciting. We learn about the different steps and considerations involved in an RNA-Seq workflow. You will also learn step-by-step pipeline executions of the entire RNA-seq differential gene expression workflow. Familiarity with GALAXY server for the execution of RNA-seq pipeline will be introduced.

Raw Data Processing & Quality Control

In this chapter we explore what are the ways to get RNA-Seq datasets, how to preprocess the raw reads and do quality control and trimming out the bad qualities using FASTQC, FASTP, Cutadapt tools.

Mapping & Raw Reads Quantification

In this chapter we teach how to do alignment of the reads against reference genome, visualization and evaluation of the alignment using HISAT2 and IGV browser.

Finding DEGs with DESeq2 & Functional Analysis

In this chapter we teach how to use DESeq2 package to find differentially expressed genes and how to do functional analysis of the DEGs.

Why Learning RNA-Seq Data Analysis Using GALAXY 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. GALAXY is a very important and easy to use server suite that allows the execution of many Bioinformatics pipelines without the need of a good computing power from the user’s end. You can create an account on GALAXY and get started with the analysis right away without needing any system requirements on your part. That’s why learning GALAXY along with RNA-seq data analysis can help you in your career greatly.

How Will this Course Benefit You?

This course provides in-depth knowledge and introduction to RNA-seq data analysis and its workflow, also covers the biological concepts of RNA sequencing. If you lack any prior knowledge of RNA-seq or have a little knowledge RNA-seq data analysis, then this course is a perfect fit for you, as this course requires no prior knowledge of either coding, RNA-seq or Bioinformatics! You will first go through a few lectures on introduction to RNA-seq, RNA-seq workflow and GALAXY which will create your foundation for RNA-Seq Data Analysis and by the end of this course, you will have a greater understanding of practical RNA-Seq Data Analysis. You don’t require any prior knowledge; you will learn every little topic for RNA-Seq data analysis pipeline 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 is RNA-Seq and how the analysis is performed
  • What is NGS & GALAXY suite
  • In-depth theoretical and practical knowledge of RNA-Seq Data Analysis
  • FASTP, FASTQC, Cutadapt for Quality Control
  • HISAT2 for Mapping/Alignment and IGV for Visualization and Evaluation
  • StringTie for Read Quantification
  • DESEQ2 for Differential Gene Expression
  • Functional Enrichment Analysis

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.
  • 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 learn how to upload your own datasets on GALAXY suite.
  • 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 how to do mapping/alignment against a reference genome using HISAT2.
  • 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 to identify differentially expressed genes using the read 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 Practical RNA-Seq Data Analysis With GALAXT is absolute beginners who have no prior experience in RNA-Seq or Bioinformatics. 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. The access to the dataset will be provided in the course dashboard.

Is It An In-Depth Theoretical and Practical Course?

Yes, everything is covered in-depth, each lecture topic duration ranges from 5-15 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 RNA-Seq or Bioinformatics?

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 R package that is highly utilized these days, DeSeq2.

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 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 & Galaxy
Quality Control and Trimming Using FASTQC, FastP, Cutadapt
Mapping With HISAT2 & Evaluation of Alignment
Discovering DEGs with StringTie, DESeq2
Functional Analysis with Gene Ontology & KEGG Pathways


  • No prior Bioinformatics or programming knowledge.
  • For beginners and advanced learners.
  • Biology background required
  • No Prior Knowledge of RNA-Seq Required

Target Audience

  • Life Sciences students and researchers
  • People working on differential gene expression
  • People looking to implement RNA-seq in their research projects
  • People who need to discover differential gene expressions in their dataset


11 Lessons3h

Introduction to NGS, RNA-Seq Pipeline & GALAXY

Introduction to Next Generation Sequencing & RNA-Seq12:09Preview
RNA-Seq Data Analysis Workflow1:20
What is Galaxy4:11
How to Get Started With Galaxy Account1:01

Practical RNA-Seq Differential Gene Expression Analysis


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30% off
All Levels
Duration 3 hours
11 lectures

Material Includes

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

Enrolment validity: 365 days

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