SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Correlation Coefficient between ChIP-seq replicates abmmki Bioinformatics 2 12-29-2016 09:59 AM
CASIM: ChIP-Seq Replicates casim UK - Cambridge 0 04-18-2013 01:20 PM
ChIP-seq peak calling from replicates ttnguyen Bioinformatics 4 08-10-2011 02:21 AM
ChIP-Seq Biological Replicates LouDore General 0 08-11-2009 12:35 PM
some questions about ChIP-Seq replicates/controls hongyan Epigenetics 3 09-24-2008 01:07 PM

Reply
 
Thread Tools
Old 09-09-2013, 07:08 AM   #1
feralBiologist
Member
 
Location: UK

Join Date: Jun 2011
Posts: 61
Default Replicates in Chip-Seq

I have the following dataset:

wild type:

2 male biol ChIP replicates for TF A
2 female biol ChIP replicates for TF B
1 male ChIP sample for TF C
1 male ChIP sample for TF D
1 male input sample (from one of the animals used for one of the samples for TF A)
1 female input sample (from one of the animals used for one of the samples for TF A)
knockouts:

1 male ChIP sample for TF A
1 pooled (male+female) ChIP sample for TF B
All animals are of similar age.

The main interest is the contrast between knockouts and wild types for TF A and TF B. I have the following questions:

(1) Does it make sense to take into account the samples for TF C and TF D?

(2) Does it make sense to take into account the sex (no sex-specific is effect is specifically expected)?

(3) How to make the best possible use of this data and which tool would you recommend? I have used macs. I am also aware about DiffBind, MEDIPS, diffreps and DBChIP but haven't used any of them so any specific recommendation regarding a tool and a workflow (if more than one tool is to be used) is most welcome.

ps. I cross-posted this on biostars: http://www.biostars.org/p/80829/
feralBiologist is offline   Reply With Quote
Reply

Tags
chip-seq, replicates

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 09:28 AM.


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