ChIP-seq Analysis using R
This tutorial aims to help analyse data from ChIP-seq experiments in bacteria that investigate the binding of transcription factors.
The tutorial will cover:
- Installing Bioconductor and bioconductor packages
- Accessing and creating genome packages
- Interacting with genome data
Aligning to a reference genome
- Aligning fastq files to your reference genome
- Checking alignment stats and quality
- Calling peaks using MACS
- Exporting and visualising peak data
- Finding transcription factor motifs from called peaks
- Overview plots
- Distance from TSS
- Functional analysis
- Coverage plots
About
This was built in R markdown which is an easy-to-use, human readable markdown language. It is particularly useful because you can include R code whenever you like and throughout you will see sections of code so that you can a) see what code has been run and b) copy and use it yourself.
I decided to bring together the tools that I have used to analyse ChIP-seq data because there is an abundance of information online for ChIP-seq analysis of eukaryotes, but not prokaryotes.