I want to quantitatively compare ChIP-seq data!
Experimental condition: - same background cell line but samples differ (WT, KO1) - same antibody was used to pull down transcription factor (not histone) - identical library preparation and sequencing parameters
My goal is to perform a differential binding analysis between the two samples (I have multiple biological replicates per condition). Considering I am looking at a transcription factor and have multiple biological replicates, which differential binding analysis is the most reliable for whole genome differential binding analysis?
I have checked out two review papers: 1. Shiqi Tu et al. An introduction to computational tools for differential binding analysis with ChIP-seq data 2. Sebastian Steinhauser et al. A comprehensive comparison of tools for differential ChIP-seq analysis
Based on their flow charts I have following options: -diffReps-nb -MultiGPS -PePr -ChIPDiff -ODIN -THOR
I am not sure if any of these are what I am looking for, so any help would be appreciated!