Go Back   SEQanswers > Applications Forums > Epigenetics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Negative control sequencing captainentropy Epigenetics 22 03-03-2016 01:16 PM
Problem with Cuffcompare to integrate different annotation sources Trudy Bioinformatics 1 03-30-2013 10:23 PM
How to integrate GeneMark.hmm results into Artemis? Caro241 Bioinformatics 1 11-06-2012 09:56 AM
How to integrate Trim Galore in Galaxy? sachitad RNA Sequencing 2 10-19-2012 02:54 AM
negative control or not ronindan Epigenetics 6 12-07-2010 01:00 AM

Thread Tools
Old 04-04-2013, 01:24 AM   #1
Location: Japan

Join Date: Mar 2013
Posts: 17
Default When to integrate the negative control?

Dear all,

I am working on a transcription factor Chip-Seq analysis that includes the following samples:
1. IP replicate 1
2. IP replicate 2
3. IgG negative control
4. Input

When is it suitable to include the IgG in the analysis process?
By that I mean, once I have called peaks of my replicates vs the Input, should I call peaks in IgG vs Input, or/and does it make sense to call peaks in the replicates vs IgG?
My first guess would be to call peaks all samples vs the Input and then substract the peaks found in IgG, but any comment is much appreciated!
Tobikenobi 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 09:55 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO