arielmadr/micm_chip_seq

MiCM ChIP seq

This workshop will guide you through the basics of ChIP-seq analysis with hands-on exercises. Participants will learn how to process ChIP-seq data: perform read alignment, peak calling, visualization through the genome browser, motif finding and gene set enrichment analysis.

Data download

You can download the data/scripts needed for this workshop in here.

Instructions

There are two options to install the software: Manual or Docker. This page covers the instructions to install manually and is the recommended option. If you are familiar with Docker and have already installed Docker, you can follow the indications in here.

Requirements

We will be using the unix terminal to run our analyses, so be sure you have access to one.

• Mac OS and any linux distribution will have a terminal already
  • Mac OS: search for terminal in your spotlight search
• Windows users:
  • Download a unix subsystem (WSL)

Sofware

• Python3 (>=3.6) is required for installing MACS2 and Deeptools
• R (>=4.0.0) and Rstudio
• Bowtie2
• Samtools
• MACS2
• Bedtools
• Deeptools

To install the software, look at the instructions for your operating system. Open your terminal and copy and paste the following commands inside the text boxes.

Linux distribution and Windows with WSL

Most of the software we need is availble through the package manager.

sudo apt install bowtie2
sudo apt install samtools
sudo apt install bedtools
pip3 install deeptools
pip3 install MACS2 # Note: For users of python 3.10 please see below

If you are using python (>=3.10), please install MACS3

pip3 install MACS3

Mac OS

First install Homebrew or any other package manager.

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Then you can use brew to install the packages.

brew install bowtie2
brew install samtools
brew install bedtools
pip3 install deeptools
pip3 install MACS2  # Note: For users of python >=3.10 please see below

If you are using python (3.10), please install MACS3

pip3 install MACS3

R libraries

This will be needed for all platforms. In R, install the dependencies:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ChIPQC")
BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene")
BiocManager::install("rGREAT")

Check the installation

To check that the program works, you can check if the help message gets printed:

bowtie2 --help
samtools --help
bedtools --help
macs2 --help # or macs3 --help
deeptools --help

Check the tutorials

• 01 - Alignment
• 02 - Peak calling
• 03 - QC
• 04 - Visualization
• 05 - Motif enrichment

If you run into any issues, you can join the pre-workshop session online.