Question: Visualizing a bigwig ChIP-seq file over a region determined by a bed ChIP-seq file
0
gravatar for topalsalih
5 months ago by
topalsalih0
topalsalih0 wrote:

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!

ADD COMMENTlink modified 5 months ago • written 5 months ago by topalsalih0

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?

ADD REPLYlink written 5 months ago by Friederike6.7k

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.

ADD REPLYlink modified 5 months ago • written 5 months ago by ATpoint45k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1770 users visited in the last hour
_