Chip-seq data analysis: from quality check to motif discovery and more

Lausanne, 27 April - 1 May 2015

Author: Giovanna Ambrosini, Philipp Bucher

Introduction

This first practical session is a kind crash course in ChIP-seq data analysis. You are asked to go to through section 1 to 6 of our which is posted on the ChIP-Seq server home page: under the heading "Documentation" (near lower left corner).

This tutorial contains step-by-step recipes for the most important data analysis tasks that can be accomplished with the ChIP-Seq and SSA servers. Try to understand each step and ask the assistants for explanations if necessary. If you finish before the lunch break, you may repeat some of the exercises with another ChIP-seq data set, or with other parameter combinations.

The tutorial includes composite figures containing the result form several ChIP-seq or SSA server tasks. For your convienence, we post an example of an R recipe to make such a figure. To run the codel you need to first download the following files:

R code for making composite Figure: Show Hide

jpeg("fig_STAT1_motif_enrichment_oprof_rmsk.jpg",
width = 1000, height = 1000, quality = 100, pointsize = 28)

plot(oprof.stat1.t100, frame.plot="F",
xlab="Distance to STAT1 peak centers", ylab="Frequency (%)",
col="black", lwd=4, type="l", xaxt="n", yaxt="n",
xlim=c(-500,500), ylim=c(0,100),
cex.axis=1.2, cex.main=1.3, cex.lab=1.3, cex.sub=1.3)
lines(oprof.stat1.t50, lwd=4, col="darkred")
lines(oprof.stat1.t25, lwd=4, col="blue")
lines(oprof.stat1.t12, lwd=4, col="cyan")
axis(1, at = seq(-500,500,250), lwd = 2, las=1, cex.axis=1.2, col="darkgray")
axis(2, at = seq(0,100,10), lwd = 2, las=1, cex.axis=1.2, col="darkgray")

legend(x="topright", legend=c(
"ChIP-Peak (th-100; 1521 peaks)",
"ChIP-Peak (th-50; 4443 peaks)",
"ChIP-Peak (th-25; 16332 peaks)",
"ChIP-Peak (th-12; 55921 peaks)"),
col=c("black","darkred","blue","cyan"), lty=c(1,1,1, 1), bty="n", lwd=4)
dev.off()

Enjoy!