Classifying Transposable Elements with Earl Grey TE

#BGA23/sessions#Workshop#Earl_Grey_TE#Transposable_elements#TEs#Annotation

This session may now be out of date so beware!!!

This session is part of BGA23

Session Leader(s)

Tobias Baril
SNSF Postdoctoral Fellow, Université de Neuchâtel

Find out more about me

Description

GitHub:: https://github.com/BGAcademy23/earlgrey-te

By the end of this session you will:

1. Be aware of the challenges of accurate TE annotation
2. Have experience of setting up the Earl Grey TE annotation environment
3. Have experience of annotating a genome assembly with Earl Grey, and of interpreting the results

Prerequisites

1. Basic understanding of transposable element classes
2. Basic understanding of linux operating systems, including navigating folder structures and running commands
3. Awareness of package managers might be useful (ie Conda/Docker), but not essential

!!! warning "Please make sure you MEET THE PREREQUISITES and READ THE DESCRIPTION above"

You will get the most out of this session if you meet the prerequisites above.

Please also read the description carefully to see if this session is relevant to you.

If you don’t meet the prerequisites or change your mind based on the description or are no longer available at the session time, please email tol-training at sanger.ac.uk to cancel your slot so that someone else on the waitlist might attend.

More Information

If you would like some more information about the thought process behind Earl Grey, you can check out the preprint here. Alternatively, you can get an idea of the interface and output files by checking out the Earl Grey Github Repository.