Introduction to ChIP-seq using high performance computing

Audience Computational Skills Prerequisites Duration
Biologists Beginner/Intermediate None 3-day workshop (~19.5 hours of trainer-led time)

Description

This repository has teaching materials for a 3-day Introduction to ChIP-sequencing data analysis workshop. This workshop focuses on teaching basic computational skills to enable the effective use of an high-performance computing environment to implement a ChIP-seq data analysis workflow. It includes an introduction to shell (bash) and shell scripting. In addition to running the ChIP-seq workflow from FASTQ files to peak calls and nearest gene annotations, the workshop covers best practice guidlelines for ChIP-seq experimental design and data organization/management and quality control.

These materials were developed for a trainer-led workshop, but are also amenable to self-guided learning.

Learning Objectives

  1. Understand the necessity for, and use of, the command line interface (bash) and HPC for analyzing high-throughput sequencing data.
  2. Understand best practices for designing a ChIP-seq experiment and analysis the resulting data.

Lessons

Click here for links to lessons and the suggested schedule

Dataset

Installation Requirements

Download the most recent versions of R and RStudio for your laptop:

NOTE: When installing the following packages, if you are asked to select (a/s/n) or (y/n), please select “a” or “y” as applicable.

(1) Install the below packages on your laptop from CRAN. You DO NOT have to go to the CRAN webpage; you can use the following function to install them:

install.packages("BiocManager")
install.packages("tidyverse")

Note that these package names are case sensitive!

(2) Install the below packages from Bioconductor. Load BiocManager, then run BiocManager’s install() function 7 times for the 7 packages:

library(BiocManager)
install("insert_first_package_name_in_quotations")
install("insert_second_package_name_in_quotations")
& so on ...

Note that these package names are case sensitive!

ChIPQC
ChIPseeker
DiffBind
clusterProfiler
AnnotationDbi
TxDb.Hsapiens.UCSC.hg19.knownGene
EnsDb.Hsapiens.v75
org.Hs.eg.db

NOTE: The library used for the annotations associated with genes (here we are using TxDb.Hsapiens.UCSC.hg19.knownGene and EnsDb.Hsapiens.v75) will change based on organism (e.g. if studying mouse, would need to install and load TxDb.Mmusculus.UCSC.mm10.knownGene). The list of different organism packages are given here.

(3) Finally, please check that all the packages were installed successfully by loading them one at a time using the library() function.

library(tidyverse)
library(ChIPQC)
library(ChIPseeker)
library(DiffBind)
library(clusterProfiler)
library(AnnotationDbi)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(EnsDb.Hsapiens.v75)

(4) Once all packages have been loaded, run sessionInfo().

sessionInfo()

These materials 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.