Harvard Chan Bioinformatics Core’s Workshops for Spring 2019

We are excited to announce the launch of HBC’s new training program for 2019!

This semester we are piloting a new learning model that replaces the 3-day workshops we have previously offered for eligible researchers.

While all of the content will remain the same as past workshops, we are changing the format to be more modular. We have divided our training content into the two categories listed below. Any participants wanting to take an advanced workshop will have to have taken certain basic workshop(s) within the past 6 months.

Spring 2019 Schedule

We are structuring the training schedule such that it gives interested researchers several opportunities to take the basic workshops.

Topic Category Date Duration Prerequisites
Introduction to the command-line interface (shell) Basic January 17th 1 day None
Introduction to R Basic January 28th & 29th 1.5 days None
Introduction to the command-line interface (shell) Basic February 13th 1 day None
Introduction to (bulk) RNA-seq Advanced February 27th and 28th 2 days Intro to shell
Introduction to R Basic March 12th and 13th 1.5 days None
Introduction to differential gene expression analysis (bulk RNA-seq) Advanced April 1st and 2nd 2 days Intro to R
Introduction to the command-line interface (shell) Basic April 11th 1 day None
Introduction to ChIP-seq analysis Advanced April 29th and 30th 2 days Intro to R & Intro to shell

Basic Data Skills

These are short 1-1.5 day workshops that provide an introduction to computational skills required for someone to get started with analyzing high-throughput sequencing data independently. These have no prerequisites and do not require any prior experience with programming.

We will alternate between two basic topics in the schedule, with at least one basic offering every month. The completion of one or more of these workshops is required in order to register for the workshops on advanced topics.

Introduction to command-line interface (Unix/shell/Linux/bash)

In this 1-day hands-on workshop, participants will learn basic commands for navigating the file system, exploring file contents, and performing basic operations, such as moving, copying, and renaming files/folders. In addition, participants will get an introduction to high-performance computing (HPC).

Introduction to R

This 1.5-day workshop will introduce participants to the basics of using R and RStudio, a simple programming environment that enables the effective handling of data, while providing excellent graphical support.

Participants will learn how to use R for:

Advanced Topics: Analysis of high-throughput sequencing (NGS) data

These are 2-day intensive workshops that instruct participants on how to efficiently manage and analyze data, with a focus on the workflow for a specific type of next-generation sequencing data (i.e RNA-seq, ChIP-seq). These workshops require participants to have taken one or more of the Basic Data Skills workshops as listed in the table below.

Topic Prerequisites
Introduction to (bulk) RNA-seq using High-Performance Computing Introduction to shell
Introduction to Differential Gene Expression Analysis Introduction to R
Introduction to ChIP-seq Analysis Introduction to R & Introduction to shell
Introduction to single cell RNA-seq Analysis Introduction to R & Introduction to shell

RNA-seq Analysis (from raw data to gene expression counts)

This 2-day hands-on workshop will cover the basics of bulk RNA-seq analysis; from designing a good experiment to performing QC on sequencing data to obtaining gene expression matrices. All the analysis will be performed on HMS-RC’s O2 cluster.

Differential Gene Expression Analysis (using gene expression counts from the above workshop)

This 2-day hands-on workshop will cover the statistical considerations when using RNA-seq data for differential gene expression analysis, followed by using DESeq2 to obtain lists of differentially expressed (DE) genes. In addition, this workshop will cover tools that will enable broader functional analysis on the DE gene lists. All the analysis will be performed using R (RStudio).

ChIP-seq analysis

This 2-day hands-on workshop will cover the basics of ChIP-seq analysis; from designing a good experiment to peak calling and performing a multitude of QC steps. This workshop requires participants to have a working knowledge of both R and shell, since we will be using HMS-RC’s O2 cluster for some of the work and doing other analyses locally.

Single cell RNA-seq

This workshop will be either 2 or 3 days long and will be offered in Summer 2019. This workshop also requires participants to have a working knowledge of both R and shell. More details coming soon!