Visualizing a bigwig ChIP-seq file over a region determined by a bed ChIP-seq file

Question

[topalsalih]

Hi everyone,

I have two ChIP-seq files. One is a bed ChIP-seq file for protein X. The second is a bigwig ChIP-seq file for another protein (protein Y). How can I extract the data from bed file to sort it from highest to the lowest occupancy? This would be the x-axis. Then, I want to plot bigwig file in the y-axis to see the values for protein Y corresponding to the locations for the protein X (from highest to lowest). Any help is greatly appreciated. Thanks!

[Friederike]

You need to provide more details about the content of the BED and BIGWIG file. Does the BED file contain occupancy values?

I'm also having a hard time envisioning the type of plot you're after. Can you perhaps link to an example plot?

[ATpoint]

Something like a profile plot maybe? Using EnrichedHeatmap for visualization of NGS experiments This tutorial uses rtracklayer in R to import a bigwig file, restricted to those regions (from a BED) you are interested in, making it fast and memory-efficient.