Metatranscriptomics

This hands-on, online course teaches data analysis for metagenomics projects. It is aimed at those with little or no experience of using high performance computing (HPC) for data analysis. In the course we will cover:

The course is taught as a mixture of live coding, online lectures, self-study and drop-in sessions.

Prerequisites

Biological concepts and software setup

This course assumes no prior experience with the tools covered in the workshop but learners are expected to have some familiarity with biological concepts, including the concept of genomes and microbiomes. Participants should bring their own laptops and plan to participate actively.

To get started, follow the directions in the “Precourse Instructions” tab to get access to the required software and data for this workshop. Windows users need to install Git Bash in their laptop. Mac users may need to configure the terminal program in their laptop to use the Bash shell.

Data

About the data used in the course

This course uses data from a 2022 paper published in BMC Environmental Microbiome titled In-depth characterization of denitrifier communities across different soil ecosystems in the tundra. In this course we will compare data from two of the sites studied.

You can read more about the data used in the course here.

Course format

This workshop is designed to be run on pre-imaged Amazon Web Services (AWS) instances. All the software and data used in the workshop are hosted on an Amazon Machine Image (AMI). We will give you details as to how to access these instances after registration.

The course will take place over three weeks and will combine live coding and teaching with offline work. We will guide you through the analysis each session but some steps may need to completed offline due to the amount of time they take to complete. There will also be drop-in sessions to offer support and troubleshooting help, and a Slack workspace for questions.

Course Overview

Lesson Overview
Files and Directories Learn about files and directories, log onto a cloud instance and get a basic introduction to the shell.
Using the Command Line Learn more about using the shell to navigate directories, manipulate and search files, and combine existing commands to do new things.
QC & Pre-Processing How to quality control raw RNA reads and prepare them for further analysis.
Taxonomic Annotation How to extract the community profile from RNA reads.
Functional Annotation How to find out which genes and pathways are present in our community.
Combining Annotations How to combine taxonomic and functional annotations for deeper understanding.
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