Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
ChIP-Seq: Normalization of ChIP-seq data with control. Newsbot! Literature Watch 0 08-14-2012 03:00 AM
Help pls! Data normalization for ChIP-seq under different conditions lavagirl Bioinformatics 2 05-10-2012 05:07 PM
ChIP-Seq: Analyzing ChIP-seq Data: Preprocessing, Normalization, Differential Identif Newsbot! Literature Watch 0 12-02-2011 05:51 AM
ChIP-Seq Data Analysis and Normalization snape_ar Bioinformatics 0 10-25-2011 01:16 PM
normalization of ChIP-seq data tanasabogdan Bioinformatics 5 08-22-2011 02:43 PM

Thread Tools
Old 05-24-2013, 01:11 PM   #1
Senior Member
Location: Bethesda MD

Join Date: Oct 2009
Posts: 499
Default proper normalization of ChIP-Seq data

We're comparing a histone modification in control samples vs. experimental samples in which the modifying enzyme is overexpressed. Western blotting indicates ~3X increase in the amount of modified histones, and qPCR of ChIPed material shows a similar increase for known target sites. Comparison of ChIP-Seq data sets indicate that the distribution of the modification is unchanged (i.e., the same peaks are detected in control and experiment). This result was anticipated by other experiments, so nothing earth-shattering.

The question: what is the appropriate method/algorithm for normalizing the ChIP-Seq data that demonstrates the enrichment we observe at these identical peaks? Most of the available tools seem designed for detecting different peaks, using the same (normalized) number of reads. In our case, however, such normalization essentially suppresses the difference in magnitude we detect by the other methods.

I'd appreciate suggestions from the more statistically-savvy members of the community.


Last edited by HESmith; 05-24-2013 at 01:17 PM. Reason: clarification
HESmith is offline   Reply With Quote
Old 09-02-2013, 02:57 AM   #2
aurélie teissandier
Junior Member
Location: paris

Join Date: Sep 2012
Posts: 1

Hi Harold,

I have the same problem. Do you have an answer to your question? Which method do you use to compare your different samples?

aurélie teissandier is offline   Reply With Quote
Old 09-02-2013, 07:50 AM   #3
Location: UK

Join Date: Jul 2012
Posts: 23

To investigate differences between peaks at the same positions I use DiffBind. It looks like you have already done peak occupancy analysis, the next step would be binding affinity analysis. Binding affinity analysis is basically investigation of differences in enrichment at same peaks across different samples - seems to be exactly what you are after. DiffBind is an R package and is actually quite easy to use and does not require a lot of expertise in R.
mknut is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 11:17 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO