Upcoming Workshop Announcement

3-Day Online Workshop on RNA-Seq Data Analysis (Reference-Based & De Novo)

Dates: January 18, 24 & 25, 2026 (Weekends)
Time: 6:00 PM – 7:30 PM (IST)
Mode: Online (Google Meet)

1. Workshop Overview

This 3-day intensive online workshop is designed to provide participants with a complete understanding of RNA-Seq data analysis workflows: both reference-based and de novo. Starting from raw sequence retrieval to PPI (Protein–Protein Interaction) analysis, the workshop covers every critical step with hands-on demonstrations, detailed instructions, and practical case studies.

Participants will learn how to fetch datasets from NCBI, assess raw data quality, perform trimming and filtering, carry out de novo assembly, map reads to a reference genome, quantify transcripts, perform differential gene expression (DEG) analysis, functional annotation, KEGG/GO analysis, and finally protein–protein interaction analysis.

This workshop is ideal for students, scholars, teachers, and early-career researchers working in genomics, transcriptomics, plant or animal sciences, biotechnology, and bioinformatics.

2. Registration Details

• Students: ₹800

• Scholars/PhD Candidates: ₹900

• Teachers/Faculty: ₹1000

A certificate of participation will be provided to all registered participants.

Registration link: https://forms.gle/JRfBxcWX8iCArRko7 

3. Workshop Topics & Schedule

📅Day 1: January 18, 2025

Module 1: Introduction & Data Retrieval

Time: 6:00 PM – 7:30 PM

Topics Covered:

• Introduction to RNA-Seq technology and workflows

• Types of RNA-seq analyses: Reference-based vs De Novo

• Overview of online sequence databases (NCBI SRA, ENA, DDBJ)

• Retrieving raw FASTQ data using:

  • NCBI SRA Toolkit (fastq-dump / fasterq-dump)

  • Direct download options (ENA links, wget commands)

• Understanding metadata, BioProject, BioSample, and SRA IDs

• Folder organization and project setup practices

📅 Day 2: January 24, 2025

Module 2: Quality Check, Trimming, Mapping & Assembly

Time: 6:00 PM – 7:30 PM

Topics Covered:

A. Quality Assessment & Preprocessing

• Quality assessment using FastQC

• Interpreting Per base quality plots, adapter content, k-mer analysis

• Quality trimming using:

  • Trimmomatic / fastp

• Generating combined QC reports using MultiQC

B. De Novo Transcriptome Assembly

• Introduction to de novo assembly concepts

• Choosing assemblers: Trinity, SPAdes RNA, rnaSPAdes

• Running Trinity step-by-step

• Evaluating assembly quality (N50, BUSCO checks)

C. Reference-Based Mapping & Quantification

• Introduction to reference genome retrieval (Ensembl, NCBI)

• Indexing reference genomes using:

  • HISAT2

  • STAR (overview)

• Mapping reads to the reference genome

• Converting SAM → BAM → sorted BAM (samtools)

• Transcript quantification using:

  • featureCounts

  • Salmon/Kallisto (quantification-only workflows)

📅 Day 3: January 25, 2025

Module 3: Differential Expression, Annotation & PPI Analysis

Time: 6:00 PM – 7:30 PM

Topics Covered:

A. Differential Gene Expression Analysis

• Introduction to count matrices and normalization concepts

• Overview of R-based DEG tools:

  • DESeq2

  • edgeR

• Volcano plot, MA plot, heatmap, PCA

• Identifying upregulated and downregulated genes

B. Functional Annotation & Pathway Interpretation

• Annotating transcripts using UNIPROT and DAVID database

• GO analysis (BP, CC, MF)

• KEGG pathway mapping (KOBAS, KAAS)

C. Protein–Protein Interaction (PPI) Analysis

• Using STRING database for PPI network exploration

• Exporting networks for downstream analysis (Cytoscape-friendly)

• Identification of hub genes and important modules

4. Required Software & Tools

Participants are encouraged to install the following before Day 1:

• SRA Toolkit

• FastQC, MultiQC

• Trimmomatic or fastp

• HISAT2 / STAR

• SAMtools

• Trinity

• R (latest version) with packages:

  • DESeq2

  • edgeR

  • ggplot2

  • pheatmap

• Cytoscape (optional for PPI visualization)

5. Who Should Attend?

• Students (BSc/MSc)

• Scholars/PhD researchers

• Teachers/Faculty

• Researchers in life sciences, biotechnology, agriculture, microbiology, or bioinformatics

No prior programming experience is required, but familiarity with basic Linux commands will be helpful.

6. Outcomes of the Workshop

By the end of this 3-day workshop, participants will be able to:

• Download RNA-seq datasets from NCBI

• Perform raw data QC and trimming

• Carry out both reference-based and de novo transcriptome analysis

• Map reads and quantify gene expression

• Conduct differential gene expression analysis

• Interpret functional annotations and biological pathways

• Build and analyze protein–protein interaction networks

7. Certificates & Post-Workshop Support

• E-certificates will be provided to all participants

• Workshop materials (slides, datasets, commands) will be shared

• One week of post-workshop support via email/WhatsApp community

📩 For Queries:
WhatsApp: +91-8135038866
Email: negenome@gmail.com

Don't miss this chance to advance your skills in transcriptome analysis!

Best Regards,
Team Negenome Bio Solutions
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