THE 3rd VIETNAM SCHOOL OF BIOLOGY (VSOB-3)

Bioinformatics analysis for bulk RNA-seq data

December 06-08, 2024 in Quy Nhon, Vietnam

Program of VSOB-3: https://icisequynhon.com/conferences/2024/VSOB-3/program.html

Data storage of VSOB-3: https://drive.google.com/drive/folders/12pXGBLSZy4fosrH77yCPr3seUa_th97u?usp=sharing

VSOB-3 Photo: https://photos.app.goo.gl/5eCRjxF7XeZkz2Ck9

School Starting

Day 1 (06/12/2024)

Morning Section

1) Dr. Cuong presents "VIETNAM SCHOOL OF BIOLOGY (VSOB): Past, Present and Future"

2) Dr. Tran Thanh Son presents "The impacts and international extension of VSOB"

3) Dr. Deeksha Bhartiya presents "Beyond the Basics: Innovative Applications of RNA Sequencing in Research" (Keynote 1)

4) Dr. Nguyen Thuy Vy presents "Fundamental concepts of RNA sequencing experiments"

5) Dr. Nguyen Thuy Vy presents "A Guide for Designing and Analyzing RNA-Seq Data"

Afternoon Section

6) Dr. Tran Thi Thanh Tam with hands-on section "RNA-seq: Upstream Analysis Part I"

Create Galaxy account at https://usegalaxy.org.au/login/start?redirect=None

Link for training in Galaxy at https://usegalaxy.org.au/join-training/vsob3/

Input Fastq files can be downloaded from Google Drive

Input Fastq files can be downloaded from Galaxy

● Quality control - FastQC
● Trimming - qctrimming data
● Mapping

Output files from Galaxy can be downloaded via link

7) Dr. Do Hoang Dang Khoa with hands-on section "RNA-seq: Upstream Analysis Part II"

Input files from Galaxy can be downloaded via link

● Mapped post-processing
● Alignment QC

Output files from Galaxy can be downloaded via link

Day 2 (07/12/2024)

Morning Section

1) Dr. Vo Sy Nam presents "Functional-oriented analysis of multi-omics data in The Vietnam Genome Program: A Perspective"

2) Dr. Cong Luan Nguyen presents "Mapping the Future with Spatial Genomics"

3) Dr. Luu Phuc Loi, Dr. Vu Minh Thiet, Dr. Do Hoang Dang Khoa and Dao Khuong Duy with hands-on section "RNA-seq: Downstream Analysis Part I"

Data can be downloaded via the link

● Google Colab introduction: go to https://colab.research.google.com/notebook
● Bulk RNA-seq bam visulization in IGV: IGV Desktop, IGVapp, MCF10A (**.bam, **.bai), MCF7 (**.bam, **.bai)
● Recap DNA-seq
● Gene Counts

• Practice 1: Gene Quantification

Afternoon Section

4) Dr. Luu Phuc Loi, Dr. Vu Minh Thiet, Dr. Do Hoang Dang Khoa and Dao Khuong Duy with hands-on section "RNA-seq: Downstream Analysis Part II"

Data can be downloaded via the link

● Calling Differential Gene Expression (DGE)

• Practice 2: Differential Gene Expression

5) Dr. Luu Phuc Loi, Dr. Vu Minh Thiet, Dr. Do Hoang Dang Khoa and Dao Khuong Duy with hands-on section "RNA-seq: Downstream Analysis Part III"

● Gene ontology analysis
● Pathway-based Analysis

• Practice 3: Functional Analysis

Day 3 (08/12/2024)

Morning Section

1) Dr. Tran Thi Thanh Tam "Building workflow for bulk RNA-seq with Galaxy"

2) Dr. Nguyen Thi Lien Hanh presents "Recent Advances and Applications of Single cell RNA-Seq in Infectious Diseases Research"

3) Dr. Luu Phuc Loi, Dr. Vu Minh Thiet, Dr. Do Hoang Dang Khoa and Dao Khuong Duy with hands-on section "RNA-seq: Downstream Analysis Part IV"

● Bulk RNA-seq Database
● Review Bulk RNA-seq
● Group Exam

• Paper
• Paper with solution

Closing Ceremony