SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
Biological replicates for RNA-seq vpp605 RNA Sequencing 15 08-29-2014 05:30 AM
using Cuffdiff with biological replicates Jane M RNA Sequencing 0 09-01-2011 01:42 AM
overdispersion and biological replicates shilez RNA Sequencing 0 08-25-2011 07:10 PM
cuffdiff with biological replicates PFS Bioinformatics 1 06-14-2011 07:51 PM
Inconsistency between biological replicates Nicholas_ Bioinformatics 1 04-06-2011 04:18 AM

Reply
 
Thread Tools
Old 08-11-2009, 12:35 PM   #1
LouDore
Junior Member
 
Location: Chicago, IL, USA

Join Date: May 2009
Posts: 4
Default ChIP-Seq Biological Replicates

How are people handling biological replicates in ChIP-Seq experiments?

I recognize the benefit of analyzing replicates independently, but what is the "best" way to then combine this data and end up with a single list of bound regions/peaks? As peak calls tend to vary by a few bases, a simple intersect of the data doesn't seem to be the best idea.

However, combining the data pre-analysis concerns me also, as there is the (unlikely) possibility of a "strong" false peak in one dataset that may make its way through the analysis despite the fact that it doesn't exist in the replicate dataset...

Hope that's clear -- if not, I'm happy to attempt to clarify my situation.

Thanks!

(In case it's not painfully obvious from my post, I am NOT a bioinformatician or programmer in any way...."just" a biologist who's not afraid of the command line. BTW, this site a great resource -- I've read nearly everything on this site and may have even understood some of it.)
LouDore is offline   Reply With Quote
Reply

Tags
biological replicates, chip-seq

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 10:25 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO