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Genome Annotation

Schedule:

Day 1

  • Morning:
    1. Introduction to Galaxy Part1 and Part2
    2. Presentation Prokaryotic annotation here
    3. Prokaryotic annotation practice here
  • Afternoon:
    1. Prokaryotic annotation practice here

Day 2

  • Morning:
    1. Presentation Eukaryotic annotation here
    2. Eukaryotic annotation practice here
  • Afternoon:
    1. Eukaryotic annotation practice here

Day 3

here

  • Morning:
    1. All-round genome annotation presentation
    2. Beginning Project
  • Afternoon:
    1. Project work

Day 4

here

  • Morning:
    1. Project work
  • Afternoon:
    1. Presentation of project

Galaxy

Galaxy set up

  1. Register to usegalaxy.eu.

Galaxy1

Galaxy2

Galaxy3

  1. Click the verification link you will receive by email.

  2. Go to this link to join our training session. It should say you successfully registered in HEHANNOT

Galaxy4

Galaxy introduction

Slides here

We will follow this tutorial

Bioconda and Conda installation

We will follow the installation recommended by bioconda directly

Installation of bioconda

  1. Install conda

Bioconda requires the conda package manager to be installed. If you have an Anaconda Python installation, you already have it. Otherwise, the best way to install it is with the Miniconda package. The Python 3 version is recommended.

On MacOS, run:

curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
sh Miniconda3-latest-MacOSX-x86_64.sh

On Linux, run:

curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh

Follow the instructions in the installer. If you encounter problems, refer to the Miniconda documentation.

  1. Set up channels

After installing conda you will need to add the bioconda channel as well as the other channels bioconda depends on. It is important to add them in this order so that the priority is set correctly (that is, conda-forge is highest priority).

The conda-forge channel contains many general-purpose packages not already found in the defaults channel.

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
  1. Install packages

Browse the packages to see what’s available.

Bioconda is now enabled, so any packages on the bioconda channel can be installed into the current conda environment:

conda install bwa

Or a new environment can be created:

conda create -n aligners bwa bowtie hisat star

!!!! if you are on ubuntu in WSL you might get an HTTP error, to solve it a simple reboot of your computer is enough.!!!!

Tutorial, guides, and CheatSheet

Here is a collection of materials to train and improve your conda use. All have their strength and weaknesses, the cheatsheet is your best friend when working.

Grade breakdown

  • 40% Active participation
  • 20% Project report
  • 40% Project presentation and discussion