README.md

# Analyzing ChIP-Seq data with Galaxy

This is the material for the galaxy workshop on chip-seq data at EMBL Rome. This is the first time that this workshop is proposed. We will start with a 2 days time frame and will adjust.

All materials used in this workshop are on the [Galaxy training website](https://galaxyproject.github.io/training-material/).


## What is Galaxy?

**Slides**: [Introduction to Galaxy](https://galaxyproject.github.io/training-material/topics/introduction/slides/introduction.html#1).

## Galaxy at EMBL

EMBL has its own instance of Galaxy at [https://galaxy.embl.de/](https://galaxy.embl.de/).

=> Demo of data import at EMBL.

## Introduction to Genomics and Galaxy

This practical aims to familiarize you with the Galaxy user interface. It will teach you how to perform basic tasks such as importing data, running tools, working with histories, creating workflows, and sharing your work.

**For this workshop of September 2019, ignore the "Log in to Galaxy" section. We are going to use the EMBL instance.**

**Tutorial**: [Introduction to Genomics and Galaxy](https://galaxyproject.github.io/training-material/topics/introduction/tutorials/galaxy-intro-strands/tutorial.html).

## Manipulating your first genomic data

In this section we will look at practical aspects of manipulation of next-generation sequencing data. We will start with Fastq format produced by most sequencing machines and will finish with SAM/BAM format representing mapped reads.

**Tutorial**:[Manipulating NGS data with Galaxy](https://galaxyproject.org/tutorials/ngs/).