Chipseq data with Mock, Input And IP
1
0
Entering edit mode
6.2 years ago

Hello Everyone,

I have ChIPseq data with two control MOCK and Input. 

I have called peaks(using MACS2) by two way as given below:

1) IP Vs Input

2) IP Vs Mock

But for downstream analysis I want to select True positive peaks or how should I filter these two peaks conditions for downstream analysis 

ChIP-Seq • 2.9k views
ADD COMMENT
0
Entering edit mode
6.2 years ago
Ian 5.7k

Given your experimental set up the easiest route is to compare the peaks from comparison 1 against the peaks found in comparison 2.  By compare I mean compare the overlap of binding region coordinates, using bedtools intersect or GALAXY intersect.

If you use MACS2 for peak calling and use the SPMR parameter you can visualise the read coverage normalised to millions of reads in UCSC browser or IGB or IGV.

My personal opinion is that the mock antibody (IgG?) is not a good control for ChIP-seq.  This was discussed in a very informative ChIP-seq paper; P919 (last paragraph), Kiddler and Zhao 2011 (http://www.ncbi.nlm.nih.gov/pubmed/?term=21934668).

 

 

 

 

ADD COMMENT

Login before adding your answer.

Traffic: 2182 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6