Microbiome Bioinformatics Analysis

General Information

Code: BIOF-Mic101

Instructor: Dr. Mona Parizadeh (Ph.D., PDF)

Organized by: ICOIA (International Community of Iranian Academics)

Start Date:

- Esfand 15, 1403 - 7 PM IRAN

Objective: Metabarcoding and 16S rRNA gene sequencing using R

Requirements:

• Laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) with administrative privileges
• Access to Wifi
• R and Rstudio installed (instructions below)
• Excel or any text editor installed (e.g. TextWrangler, Notepad, BBEdit, etc.)

Contact: [email protected]

Register: here

To ask questions about the course, communicate with the instructor and get informed about other free training courses, become a member of the ICOIA Online School Telegram Group.

Audience

This course is suitable for:

• Levels: Beginner & Intermediate
• Fields: Biology, Medicine, Veterinary, and Agriculture & Natural Resources
• Language: Farsi

This course covers the following material:

• Introduction to metabarcoding and amplicon sequencing
• Introduction to R
• DADA2 Tutorial
• Introduction to phyloseq package in R
• Data exploration
• Statistical analyses of 16S rRNA gene sequences:
  • Taxonomic composition
  • Alpha diversity
  • Beta diversity (ordination)
  • PERmutational Multivariate ANalysis Of VAriance (PERMANOVA)
  • Differential analysis
• Discussion
  • Wrap up of the results of 16S rRNA gene sequence analysis

Setup

To participate in this Workshop, please install the following software, complete the R courses for beginners, and let us know if you need any help before attending.

Install R and RStudio

R is a free and open-source programming language that is particularly powerful for data exploration, visualization, and statistical analysis. We use RStudio to interact with R.

Windows

Please download R for Windows from CRAN to install R, and also install the RStudio IDE. If you have separate user and admin accounts, please run the installers as an administrator by right-clicking on the .exe file and selecting "Run as administrator" instead of double-clicking. Otherwise, problems may arise later when installing R packages.

Video Tutorial

Mac OS X

Please download R for macOS from CRAN to install R, and also install the RStudio IDE.

Video Tutorial

Linux (Debian, Fedora/Redhat, Ubuntu)

Please download the binary files for your distribution from CRAN to install R, or use a package manager (e.g. run sudo apt-get install r-base for Debian/Ubuntu and run sudo yum install R for Fedora/Redhat). Additionally, please install the RStudio IDE.

R for beginners

To follow the workshop, you must have a basic understanding of R. Before attending the workshop, please go through the following courses:

• Introduction to R (1)
• Introduction to R (2)
• Programming with R

Download database for taxonomic assignment with DADA2

• silva_nr99_v138.2_toGenus_trainset.fa.gz
• silva_nr99_v138.2_toSpecies_trainset.fa.gz

Download data for microbial analysis with DADA2

• mouse_demultiplexed
• mouse_metadata