RNA-Seq and Transcriptomic Data Analysis Training Course

Module 1: Introduction to Transcriptomics, Experimental Design, and Next-Generation Sequencing

ü  Overview of RNA-Seq technologies: Illumina, Pacific Biosciences (PacBio), and Oxford Nanopore

ü  Principles of experimental design: Replicates, batch effects, sequencing depth, and read length selection

ü  Total RNA vs. mRNA-seq vs. targeted transcriptomic profiling approaches

ü  Library preparation strategies, strand-specific protocols, and quality requirements

ü  Practical Session: Evaluating experimental design, power analysis, and sample size calculations using interactive computational tools

Module 2: Linux Command Line and High-Performance Computing for Genomics

ü  Essential Linux shell commands for managing large-scale genomic file formats

ü  Working with genomic file structures: FASTQ, FASTA, GTF, GFF, SAM, and BAM

ü  Managing software dependencies using Conda environments and Docker containers

ü  Shell scripting fundamentals for processing multi-sample sequencing cohorts

ü  Practical Session: Writing a Bash script to organize raw sequencing files and run batch file integrity checks

Module 3: Raw Data Quality Control, Preprocessing, and Read Trimming

ü  Understanding quality metrics in raw sequencing data (Phred scores, GC content, adapter contamination)

ü  Assessing raw FASTQ files using FastQC and summarizing cohort metrics with MultiQC

ü  Trimming low-quality bases, synthetic adapters, and overrepresented sequences using Trimmomatic and Cutadapt

ü  Post-trimming quality validation and evaluation of read filtering efficiency

ü  Practical Session: Running quality control checks on a multi-sample FASTQ dataset and generating a unified MultiQC report

Module 4: Reference-Based Read Alignment and Pseudo-Alignment Strategies

ü  Principles of spliced alignment algorithms for eukaryotic genomes

ü  Aligning reads against reference genomes using STAR and HISAT2

ü  Fast quantification via alignment-free pseudo-alignment tools (Kallisto and Salmon)

ü  Assessing alignment stats, mapping rates, and genomic coverage distribution

ü  Practical Session: Indexing a reference genome and executing STAR alignment on trimmed paired-end RNA-Seq reads

Module 5: Gene and Transcript Quantification

ü  Generating raw read counts per gene using featureCounts and HTSeq-count

ü  Normalization strategies: Understanding CPM, RPKM, FPKM, TPM, and size factors

ü  Managing multi-mapping reads, duplicated sequences, and ambiguous transcript overlaps

ü  Importing alignment-free quantification estimates into R using tximport

ü  Practical Session: Quantifying gene expression levels from mapped BAM files and constructing a count matrix in R

Module 6: Differential Gene Expression (DGE) Analysis in R

ü  Statistical foundations of DGE: Negative binomial models and dispersion estimation

ü  Performing differential expression analysis using DESeq2 and edgeR packages

ü  Identifying and adjusting for batch effects and unwanted variation using SVA and ComBat

ü  Visualizing results: Volcano plots, MA plots, sample clustering, and expression heatmaps

ü  Practical Session: Executing a complete DGE workflow in R studio to identify key differentially expressed genes with DESeq2

Module 7: Functional Enrichment, Pathway Mapping, and Systems Biology

ü  Gene Ontology (GO) annotation: Biological Processes, Molecular Functions, and Cellular Components

ü  Pathway analysis frameworks: KEGG, Reactome, and Gene Set Enrichment Analysis (GSEA)

ü  Using ClusterProfiler and fgsea packages in R for functional annotation

ü  Network analysis and protein-protein interaction (PPI) mapping with Cytoscape

ü  Practical Session: Conducting GSEA and generating functional pathway enrichment plots for differentially expressed gene clusters

Module 8: Single-Cell RNA Sequencing (scRNA-Seq) Data Processing

ü  Introduction to single-cell RNA-Seq protocols (10x Genomics, Smart-seq2)

ü  Quality control filtering for scRNA-seq: Mitochondrial content, doublet removal, and cell filtering

ü  Normalization, feature selection, and dimensionality reduction (PCA, UMAP, t-SNE)

ü  Cell type identification using marker genes and automated annotation toolkits in Seurat

ü  Practical Session: Processing a 10x Genomics single-cell dataset in R to perform clustering and identify cell-type-specific markers

Module 9: Long-Read Transcriptomics, Isoform Analysis, and Alternative Splicing

ü  Understanding long-read RNA sequencing advantages for full-length transcript isoforms

ü  Detecting alternative splicing events (exon skipping, intron retention) using rMATS and IsoformSwitchAnalyzeR

ü  Identifying novel transcripts, fusion genes, and long non-coding RNAs (lncRNAs)

ü  Comparing short-read and long-read transcriptomic profiling accuracy

ü  Practical Session: Analyzing alternative splicing patterns across experimental conditions and visualizing exon usage diagrams

Module 10: Reproducible Research, Pipeline Automation, and Multi-Omics Integration

ü  Principles of FAIR (Findable, Accessible, Interoperable, Reusable) data management in genomics

ü  Workflow automation frameworks: Nextflow and Snakemake for RNA-Seq pipelines

ü  Integrating transcriptomic data with epigenomic (ATAC-seq) and proteomic datasets

ü  Documenting analyses using R Markdown, GitHub repositories, and public data deposition (GEO/SRA)

ü  Practical Session: Building a basic automated Snakemake workflow for an end-to-end transcriptomic processing pipeline

About Our Trainers

Our lead instructors are accomplished bioinformaticians, genomic data scientists, and molecular biologists with over 12 years of hands-on experience leading computational biology research in academic institutions, clinical genomics facilities, and biotechnology enterprises. They possess deep theoretical knowledge and practical expertise in high-throughput sequencing, cloud computing, pipeline development, and multi-omics data synthesis. Each trainer has a proven track record of authoring peer-reviewed genomic publications and delivering technical bioinformatics training to researchers worldwide.

Quality Statement

Phoenix Center for Policy, Research and Training is committed to delivering exceptional professional education that adheres to strict international standards of scientific and educational excellence. Our transcriptomic and bioinformatics curricula are continually updated to reflect the fast-paced advancements in sequencing platforms, computational algorithms, and bioinformatic software standards. We prioritize hands-on computational fluency, practical problem-solving, and rigorous quality assurance to ensure every participant gains functional skills that translate directly to real-world research environments.

Tailor-Made Courses

We understand that every organization has unique challenges and opportunities as well as unique training needs. Phoenix Training Center offers tailor-made courses designed to address specific requirements and challenges faced by your team or organization. Whether you need a customized curriculum, a specific duration, or on-site delivery, we can adapt our expertise to provide a training solution that perfectly aligns with your objectives. We can customize this Course to focus on your industry, specific risk profile, or internal stakeholder dynamics. Contact us to discuss how we can create a bespoke training program that maximizes value and impact for your team. For further inquiries, please contact us on Tel: +254720272325 / +254737296202 or Email training@phoenixtrainingcenter.com.

Admission Criteria

ü  Participants should be reasonably proficient in English.

ü  Applicants must live up to Phoenix Center for Policy, Research and Training admission criteria.

Terms and Conditions

ü  Discounts: Organizations sponsoring Four Participants will have the 5th attend Free

ü  What is catered for by the Course Fees: Fees cater for all requirements for the training – Learning materials, Lunches, Teas, Snacks and Certification. All participants will additionally cater for their travel and accommodation expenses, visa application, insurance, and other personal expenses.

ü  Certificate Awarded: Participants are awarded Certificates of Participation at the end of the training.

ü  Course Improvement: The program content shown here is for guidance purposes only. Our continuous course improvement process may lead to changes in topics and course structure.

ü  Approval of Course: Our Programs are NITA Approved. Participating organizations can therefore claim reimbursement on fees paid in accordance with NITA Rules.

Booking for Training

Kindly send an email to the Training Officer on training@phoenixtrainingcenter.com and we will send you a registration form. We advise you to book early to avoid missing a seat to this training. Or call us on +254720272325 / +254737296202

Payment Options

We provide 3 payment options, choose one for your convenience, and kindly make payments a week before the training starts (at least 5 to 7 days before the Training start date) to reserve your seat:

ü  Groups of 5 People and Above – Cheque Payments to: Phoenix Center for Policy, Research and Training Limited should be paid in advance, a week before the training starts.

ü  Invoice: We can send a bill directly to you or your company.

ü  Deposit directly into Bank Account (Account details provided upon request)

Cancellation Policy

ü  Payment for all courses includes a registration fee, which is non-refundable, and equals 15% of the total sum of the course fee.

ü  Participants may cancel attendance 14 days or more prior to the training commencement date.

ü  No refunds will be made 14 days or less before the training commencement date. However, participants who are unable to attend may opt to attend a similar training course at a later date or send a substitute participant provided the participation criteria have been met.

Accommodation and Airport Pick-up

For physical training attendees, we can assist with recommendations for accommodation near the training venue. Airport pick-up services can also be arranged upon request to ensure a smooth arrival. Please inform us of your travel details in advance if you require these services. For reservations contact the Training Officer on Email: training@phoenixtrainingcenter.com or on Tel: +254720272325 / +254737296202.