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ChIP-nexus / ChIP experiments with Nucleotide resolution through Exonuclease Unique barcode and Single ligation

A ChIP-exo protocol for map transcription factor (TF) binding genome-wide. This protocol uses an efficient DNA self-circularization step during library preparation. ChIP-nexus protocol combines the standard ChIP-exo protocol with the library preparation protocol from the iCLIP method for mapping RNA-protein interaction and a randomized barcode to the adapter which enables monitoring of over-amplification.

PeakXus

A peak caller specifically designed to leverage the increased accuracy of novel experimental methods for studying transcription factor (TF) binding in vivo in an unbiased manner. Our emphasis is on filtering out false binding events by criteria well motivated by the experimental design while avoiding any unnecessary assumptions about the outcome of the experiment. We apply PeakXus to ChIP-Nexus and ChIP-exo experiments performed both in Homo sapiens and in Drosophila melanogaster cell lines. We show that PeakXus consistently finds more peaks overlapping with a TF-specific recognition sequence than published methods.

Q-nexus

A method for the estimation of the protected-region width and peak calling that can be applied to ChIP-nexus as well as ChIP-exo data. Q-nexus creates pseudo-controls from the data with which true signal can be differentiated from pseudo-peaks, which allows us to accurately estimate the width of the protected region. Then, Q-nexus performs an analysis of the qfrag distribution to center candidate peaks and then performs a statistical analysis of the read depth distribution to identify peaks.