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The analysis of ChIP-seq samples outputs a number of enriched regions, each indicating a protein-DNA interaction or a specific chromatin modification. Enriched regions (commonly known as "peaks") are called when the read distribution is significantly different from the background and its corresponding significance measure (p-value) is below a user-defined threshold.

When replicate samples are analysed, overlapping enriched regions are expected. This repeated evidence can therefore be used to locally lower the minimum significance required to accept a peak. Here, we propose a method for joint analysis of weak peaks.

Given a set of peaks from (biological or technical) replicates, the method combines the p-values of overlapping enriched regions: users can choose a threshold on the combined significance of overlapping peaks and set a minimum number of replicates where the overlapping peaks should be present. The method allows the "rescue" of weak peaks occuring in more than one replicate and outputs a new set of enriched regions for each replicate.

For details you may refer to the project's website or MSPC publication.
Alternatively, you may check the MSPC slides on slideshare.
A linux/Mac built is available at DOWNLOADS tab.

Graphical version

MuSERA is a graphical tool that efficiently implements MSPC for comparative evaluation of ChIP-seq and DNase-seq samples. Additionally, it facilitates the assessment of replicates by integrating common pipelines such as functional analysis, nearest feature distance distribution, chromosome-wide statistics, plotting features, and an integrated genome browser.



Vahid Jalili : vahid DOT jalili AT polimi DOT it

Citing MSPC

If you use or extend MSPC in your published work, please cite the following publication:

Vahid Jalili, Matteo Matteucci, Marco Masseroli, and Marco J. Morelli
Using combined evidence from replicates to evaluate ChIP-seq peaks
Bioinformatics (2015) 31 (17): 2761-2769 first published online May 7, 2015 doi:10.1093/bioinformatics/btv293.

Last edited Apr 18, 2016 at 11:15 AM by VahidJalili, version 24