Module 1: Introduction to ChIP sequencing & analysis

Important notes:

• Please refer to the following guide for instructions on how to connect to the workshop server and required modules Using Compute Canada
• The user class99 is provided here as an example. You should replace it by the username that was assigned to you at the beginning of the workshop.

Introduction

Description of the lab

This module will cover the basics of how to login to the cluster, launch jobs and perform a basic QC analysis of the data sets.

Local software that we will use

• ssh
• Web browser to visualize FastQC output

Tutorial

Getting started

Connect to the Workshop server

ssh class99@workshop103.ccs.usherbrooke.ca

You will be in your home folder.

Prepare directory for module 1

rm -rf ~/module1
mkdir -p ~/module1
cd ~/module1

Prepare environment for module 1

module load mugqic/java mugqic/fastqc

Assessing FASTQ file quality with FastQC

Copy locally the FASTQ file that we will need for our FastQC analysis

cp /home/partage/epigenomics/chip-seq/H1/data/H3K27ac/H3K27ac.H1.fastq.gz .

Check files

At this point if you type ls should have something like:

class99@workshop103$ ls
H3K27ac.H1.fastq.gz

Check FastQC options

fastqc -h

Run the FastQC command

fastqc H3K27ac.H1.fastq.gz

Check files

At this point if you type ls should have something like:

class99@workshop103$ ls
H3K27ac.H1_fastqc.html	H3K27ac.H1_fastqc.zip  H3K27ac.H1.fastq.gz

Download the results to your local computer

From your local computer:

scp class99@workshop103.ccs.usherbrooke.ca:/home/class99/module1/H3K27ac.H1_fastqc.html .

Open the downloaded file in a web browser

Open the folder and then double-click the file you just downloaded.

Or directly from the command line using a command such as

firefox H3K27ac.H1_fastqc.html