ChIP-Seq practical

This exercise allows you to do some basic analysis of ChIP-seq data. You will align ChIP-seq data to the mouse genome using Bowtie, then find immuno-enriched areas using the peak caller MACS. You will visualise the data in a genome browser and perform annotation and motif analysis on the predicted binding regions. This task takes 1.5 to 2 hours.

 

Steps

Click here to download the files and worksheet.

Before you download this folder, be aware that it is 118.5MB

 

You will need to install the following programmes and commands on your computer in order to carry out this practical:

 

Warning

In the NGS workshop, the files were pre-installed on the course computers in specific file locations. The commands in the worksheet direct to those file locations: you will need to alter the commands to go to the locations where you have saved your files.