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RNA-Seq Course

Course cover - Foundations of RNA-Seq: From Concepts to Analysis

Foundations of RNA-Seq: From Concepts to Analysis (No Coding Required)

Course Summary

Learn the complete workflow of RNA-Seq, from essential biological principles and next-generation sequencing (NGS) concepts to practical data analysis. This no-coding course is designed for medical and biomedical learners who want to confidently perform RNA-Seq data analysis.

Course Description

This course introduces you to the world of NGS and transcriptomics in a clear, step-by-step manner. The focus is on building a broad conceptual understanding and hands-on analysis skills that empower you to perform RNA-Seq data analysis independently, without getting lost in complex statistics, technologies, or coding.

The course begins with the fundamental principles of gene expression and NGS, provides an overview of the RNA-Seq workflow, and then guides you through the complete RNA-Seq analysis pipeline using a user-friendly analysis environment that requires no coding skills.

Through detailed instructions with recorded practical videos and lectures in Bangla, live interactive sessions, curated external resources, readings, worksheets, and quizzes, you will learn to perform key steps in RNA-Seq data analysis, including quality control, read alignment, gene expression quantification, differential expression, and enrichment analysis. A real published dataset from an international peer-reviewed journal will be used throughout the course, allowing you to practice each step of the workflow in a structured, hands-on manner, and eventually reproduce the results of the published paper. In the final phase, you will complete a capstone project, presenting your findings in a format that simulates a research presentation, thus building your confidence and competence to independently perform RNA-Seq analyses.

By the end of the course, you will be able to:

  • Explain key concepts and terminology in NGS and RNA-Seq.
  • Perform RNA-Seq data analysis from raw reads to biological interpretation without any coding.
  • Present your RNA-Seq analysis results in a format that mimics a research presentation.

This course is ideal for:

Undergraduate students, graduate students, postdoctoral researchers, and professionals in medicine, biology, and related fields with no prior coding or bioinformatics experience. It is particularly beneficial for those who want to conduct research using RNA-Seq or prepare for higher studies and research opportunities, such as MS, PhD, or postdoctoral positions in competitive research programs.

Instructor:

This course will be taught by Dr. Md Anwarul Karim (Mijan), currently a Postdoctoral Researcher at Baylor College of Medicine, USA. Dr. Karim graduated with an MBBS from Chittagong Medical College and earned his PhD in Genetics from the University of Hong Kong.

Throughout his PhD and postdoctoral training, he has extensively analyzed next-generation sequencing (NGS) data, including whole-exome sequencing, bulk RNA-Seq, single-nucleus RNA-Seq (snRNA-Seq), and Xenium spatial transcriptomics datasets. During his PhD, he identified novel candidate genes associated with Hirschsprung disease using whole-exome sequencing. He is currently conducting research on Spinocerebellar Ataxia Type 1.

In addition to his doctoral and postdoctoral training, Dr. Karim has completed numerous specialized courses and workshops at internationally renowned institutions, including the Wellcome Genome Campus (Hinxton, Cambridge, UK) and the Max Planck Institute of Molecular Cell Biology and Genetics (Dresden, Germany).

Dr. Karim also has extensive experience in teaching and e-learning through his work at the University of Hong Kong and Chattogram International Medical College. He has authored more than 15 peer-reviewed research articles in international journals and has presented his research at multiple international scientific conferences.

To view the instructor’s complete curriculum vitae, please visit this page.

If you are interested in enrolling in a future batch, please fill out the form below.

RNA-Seq Course Enrollment Form

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Foundations of RNA-Seq: From Concepts to Analysis

No Coding Required

A complete RNA-Seq learning experience combining theory and hands-on analysis using real sequencing data. Below is an overview of the hands-on skills covered in the practical section.

Course Timeline

Course Timeline

Foundations of RNA-Seq: From Concepts to Analysis (No Coding Required)

Md Anwarul Karim, MBBS, PhD

Course Format

  • Hands-on practical videos (Bangla): Clear, step-by-step demonstrations of key concepts and workflows. This practical training uses a real RNA-Seq dataset from a peer-reviewed publication, allowing you to answer real biological questions just like in a published research study.
  • Curated conceptual videos (English) and recoded lectures (Bangla): This is to further enhance understanding of the RNA-Seq workflow and practical contents.
  • Interactive live sessions: To interactively discuss the key concepts and Q/A.
  • Concept notes and MCQ questions: Concise concept notes, problem-based and simple recall type MCQs to summarize key topics and self-assessment.
  • WhatsApp community support: For troubleshooting, peer learning, and faster announcements.
  • Delivered via Moodle: A learning management system widely used by top global universities.
  • Mostly flipped classroom model: The core learning content is delivered through Moodle for structured self-paced learning, while live interactive sessions are dedicated to discussing key concepts, addressing questions, and reinforcing understanding.
Course Timeline
Foundations of RNA-Seq: From Concepts to Analysis (No Coding Required)
Course Details: https://meducationonline365.com/all-courses/
Course Instructor: Md Anwarul Karim, MBBS, PhD
Application for course enrollment
Onboarding, Moodle account creation for course participants, and pre-course survey
Day-1
Moodle course access and release of initial course modules
Moodle Module 1: Molecular biology foundations
  • Biomolecules and the flow of information
  • Detection of biomolecules: Small-scale approaches
  • Detection of biomolecules: Large-scale approaches
Moodle Module 2: Next-generation sequencing (NGS)
  • Overview of NGS
  • NGS sample preparation
  • Raw sequencing data file format
Recorded Session 1: Course orientation, and fundamentals of molecular biology, NGS, and RNA-Seq

Recorded Session 2: Reference genome, WGS vs. WES vs. Target panel NGS, RNA-Seq, raw data quality control
  • Moodle Practical 1: Preparing for RNA-Seq data analysis
Day-21 | Saturday | 7:30 PM Bangladesh Time | Live session – 1
Course orientation; Fundamentals of molecular biology, NGS, & RNA-Seq
Moodle Module 3: RNA-Seq workflow
  • Overview of RNA-Seq workflow
  • The RNAverse and the mRNA enrichment methods
  • Unstranded vs. Stranded RNA-Seq
  • Moodle Practical 2: Analysis platform interface navigation and RNA-Seq data import
Day-28 | Saturday | 7:30 PM Bangladesh Time | Live session – 2
Reference genome, WGS vs. WES vs. Target panel NGS, RNA-Seq, raw data quality control, unstranded vs. stranded RNA-Seq
Moodle Module 4: Quality control of the raw sequencing data
  • Assessing sequencing data quality

Moodle Module 5: Read alignment and quantification
  • RNA-Seq reads alignment/mapping
  • Moodle Practical 3: Flattening raw RNA-Seq dataset collections and assessing raw data quality
  • Moodle Practical 4: Cleaning raw RNA-Seq data
  • Moodle Practical 5: Flattening cleaned RNA-Seq dataset collections and assessing data quality
  • Moodle Practical 6: Aligning cleaned RNA-Seq reads to the reference genome
  • Moodle Practical 7: Quantifying gene expression from aligned RNA-Seq reads
Day-35 | Saturday | 7:30 PM Bangladesh Time | Live session – 3
Conceptual overview of NGS read mapping, and BAM/SAM file format
Recorded session video: BAM/SAM visualization by IGV
Moodle Module 6: Differential gene expression analysis
  • Differential gene expression analysis
  • Moodle Practical 8: Differential gene expression analysis and annotation of results
  • Moodle Practical 9: Creating volcano plot
Day-42 | Saturday | 7:30 PM Bangladesh Time | Live session – 4
Per gene read count, differential expression analysis, PCA plot, volcano plot, and heatmap
Moodle Module 7: Interpretation and visualization of differential expression results
  • Gene set analysis: ORA and GSEA
  • Moodle Practical 10: Biological interpretation of differentially expressed genes
  • Moodle Practical 11: Heatmap, over-representation analysis (ORA), gene set enrichment analysis (GSEA)
Day-49 | Saturday | 7:30 PM Bangladesh Time | Live session – 5
Conceptual overview of Gene Ontology (GO), over-representation analysis (ORA), gene set enrichment analysis (GSEA)
Grace period
Grace period
Day-63 | Saturday | 7:30 PM Bangladesh Time | Live session – 6
Limitation of bulk RNA-Seq and the power of single cell/nucleus RNA-Seq; Presentation from course participants
Grace period
Grace period
Day-70 | Saturday | 7:30 PM Bangladesh Time | Live session – 7
Extra topics / Future directions; Presentation from course participants
Grace period
Grace period
Day-77 | Course ends

Estimated course workload

Component Approximate duration
Hands-on practical videos ~8.5 hours
Recorded sessions / Curated conceptual videos ~15 hours
Live sessions Variable
Notes / MCQs / Capstone Variable

Recommended commitment: 5 hours per week

Note: The durations shown represent the approximate total length of the video content available on Moodle. The actual time required for understanding, note-taking, and independently performing the practical exercises may vary significantly depending on individual background and learning pace.

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