SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
how to generate random size matched background regions gene_x Bioinformatics 1 07-25-2015 03:14 AM
CisGenome for de novo motif discovery hoangsa De novo discovery 0 04-18-2011 02:29 PM

Reply
 
Thread Tools
Old 09-20-2016, 10:58 AM   #1
luca88
Junior Member
 
Location: Edinburgh

Join Date: May 2015
Posts: 1
Default Background regions for de novo Motif Discovery?

Hello everyone,

I posted this also on Biostars a couple of days ago, not sure where I can find someone to help me.

I'm trying to identify the binding motif of a transcription factor based on ChIP-seq peaks identified with MACS2.

I tried different tools (among which Homer, MEME-ChIP, STEME, RSAT) but I have a couple of questions as I'm not sure about the validity/reproducibility of my results:

Do you select the peaks (for example taking the top 10-20% of the peaks ranked by fold change/p-value) or you give as input the full list of them? What's the best practice?

Do you use your own background sequences or you let the software generate its own background?

In case you use a custom background, what do you use? For example, I tried to give randomly picked regions identified by DNase-seq, but this completely abolished the enrichment of the motifs that I get when I don't give any custom background.

Thanks for your help!
luca88 is offline   Reply With Quote
Reply

Tags
background, chip-seq, homer, macs peaks chip-seq, motif finding

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 01:30 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO