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Epigenomic Data Analysis 2016

Module 1 Lab

Module 1: Introduction to ChIP sequencing & analysis

Important notes:

  • Please refer to the following guide for instructions on how to connect to Guillimin and submit jobs: Using the Guillimin HPC
  • The instructions in this tutorial will suppose you are in a Linux/Max environment. The equivalent tools in Windows are provided in the Using the Guillimin HPC.
  • 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 Guillimin HPC
ssh class99@guillimin.clumeq.ca

You will be in your home folder. At this step, before continuing, please make sure that you followed the instructions in the section “The first time you log in” of the Using the Guillimin HPC. If you don’t, compute jobs will not execute normally.

Prepare directory for module 1
rm -rf ~/module1
mkdir -p ~/module1
cd ~/module1

Assessing FASTQ file quality with FastQC

Copy locally the FASTQ file that we will need for our FastQC analysis
cp /gs/project/mugqic/bioinformatics.ca/epigenomics/chip-seq/H1/data/H3K27ac/H3K27ac.H1.fastq.gz .
Check files

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

[class99@lg-1r14-n04 module1]$ ls
H3K27ac.H1.fastq.gz
Run the FastQC command on the scheduler
echo 'module load mugqic/fastqc/0.11.2 ; fastqc H3K27ac.H1.fastq.gz' | qsub -l nodes=1:ppn=1 -d .
Check the status of the job
showq -uclass%%

Where you replace %% by your student number. It usually takes a few seconds/minutes for the job to appear depending on the load of the cluster.

Check files

At this point if you type ls should have something like

[class99@lg-1r14-n04 module1]$ ls
H3K27ac.H1_fastqc.html	H3K27ac.H1_fastqc.zip  H3K27ac.H1.fastq.gz  STDIN.e60293217  STDIN.o60293217
Download the results to your local computer
scp class99@guillimin.clumeq.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

open .

Or directly from the command line using a command such as

firefox H3K27ac.H1_fastqc.html
View on GitHub