About the Workshop Series

In this workshop, we will access a server to perform fundamental amplicon sequence analyses in QIIME2 using command line. We will then import and process the generated data into R for additional common workflows using the phyloseq and DESeq2 packages.

You will learn how to:

• log in on a server and navigate its file system.
• identify the structure and components of Unix commands.
• browse the documentation of commands.
• transfer files to and from a server.
• run jobs in the background.
• execute common steps in the QIIME2 workflow.
• use R to import QIIME 2 data as a phyloseq object and how to access its different components.
• process the phyloseq object for different avenues of analysis.
• determine what taxa are present at different levels between two groups using differential abundance analysis.
• express abundance levels as a relative abundance plot using ggplot2.
• calculate diversity metrics and plot them in R.

This workshop will take place in person, if there are any changes, we will change it to Zoom and a Zoom link will be provided to participants prior to the workshop via email.

Sessions

This is a 2 part workshop series. Your registration covers 2 sessions, totaling 6 hours of instruction.

• Day 1:
• Friday, Apr 1,1:00 - 4:00pm
• Day 2: Monday, Apr 4, 1:00 - 4:00pm

Funding and Fees

ECOSCOPE workshop fees are collected on a cost-recovery basis only. We strongly encourage students and postdocs interested to ask their research supervisors to cover these fees in order to sustain the workshop initiative. Supervisor payments can be made directly to ECOSCOPE using journal vouchers. Contact us for more information on how to effect this process.

Pre-requisites

Navigation of file system in command line, "Introduction to R" or EDUCE modules in MICB 301/405/425, or equivalent knowledge of R.

Contact

For questions or further inquires, please contact ECOSCOPE at info.ecoscope@ubc.ca. For more events, take a look at our event calendar