General Information

Description:

This 3-day hands-on workshop will instruct participants on how to efficiently manage and analyze ChIP-seq data using the command line interface and work in a high-performance computing (HPC) environment.

The workshop will begin with an introduction to the UNIX shell and basic commands, followed by an introduction to high-performance computing, specifically focused on HMS-RC's O2 cluster. Starting on the second day, the workshop will delve into the ChIP-seq workflow starting from sequence reads, including experimental design guidance for the chromatin immunoprecipitation step. Participants can expect to learn how to run a ChIP-seq data analysis workflow, including quality control, peak calling, visualization, and functional analysis steps.

No prior programming experience or command line knowledge is required.

Setup

1. Please have the following programs installed on your laptop:

Mac users

1. Java

2. Filezilla (make sure you get the Filezilla Client, not the Server)

3. Integrative Genomics Viewer (IGV)

4. Text Wrangler or Sublime Text

Windows users

1. Git Bash

2. Java

3. Filezilla (make sure you get the Filezilla Client, not the server)

4. Integrative Genomics Viewer (IGV)

5. Notepad++

2. To use O2, we will have temporary training accounts available for you to use for the duration of the workshop. But, if you do not have an account on O2, and wish to create your own account for use during class please follow the instructions below:

First, check that you are able to sign in with your an eCommons ID/Password: The eCommons login is required to create your account on O2. If you are unsure whether you have an account or forgot your password, please check using this self-service link on the eCommons website: https://ecommons.med.harvard.edu/.
After making sure that you have an eCommons login, please do the following:
1. 1. Go to: https://rc.hms.harvard.edu/#cluster
  2. Click the “Account Request” button (red). That will bring up a web-form on your screen for user account request
  3. Please fill out the required fields (Name, eCommons ID, HMS (or affiliated) email address, and Organization/Department you belong to).

Once the account gets created, you will get an email from HMS Research Computing with a confirmation.

Schedule

For this workshop schedule and materials please see the GitHub page.

Practice Exercises

Acknowledgements, Support & License:

This workshop is sponsored by the Harvard Medical School Tools and Technology Committee (TnT), the Harvard NeuroDiscovery Center (HNDC), and the Harvard Stem Cell Institute (HSCI).

These lessons have been developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC). These are open access materials distributed under the terms of the Creative Commons Attribution license (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Some of the materials used in this lesson are adapted from work that is Copyright © Data Carpentry (http://datacarpentry.org/). All Data Carpentry instructional material is made available under the Creative Commons Attribution license (CC BY 4.0).

Bioinformatics Training at Harvard Chan Bioinformatics Core

Introduction to ChIP-seq with HPC