Q-nexus

BACKGROUND: ChIP-nexus, an extension of the ChIP-exo protocol, can be used to map
the borders of protein-bound DNA sequences at nucleotide resolution, requires
less input DNA and enables selective PCR duplicate removal using random barcodes.
However, the use of random barcodes requires additional preprocessing of the
mapping data, which complicates the computational analysis. To date, only a very
limited number of software packages are available for the analysis of ChIP-exo
data, which have not yet been systematically tested and compared on ChIP-nexus
data. RESULTS: Here, we present a comprehensive software package for ChIP-nexus
data that exploits the random barcodes for selective removal of PCR duplicates
and for quality control. Furthermore, we developed bespoke methods to estimate
the width of the protected region resulting from protein-DNA binding and to infer
binding positions from ChIP-nexus data. Finally, we applied our peak calling
method as well as the two other methods MACE and MACS2 to the available
ChIP-nexus data. CONCLUSIONS: The Q-nexus software is efficient and easy to use.
Novel statistics about duplication rates in consideration of random barcodes are
calculated. Our method for the estimation of the width of the protected region
yields unbiased signatures that are highly reproducible for biological replicates
and at the same time very specific for the respective factors analyzed. As judged
by the irreproducible discovery rate (IDR), our peak calling algorithm shows a
substantially better reproducibility. An implementation of Q-nexus is available
at http://charite.github.io/Q/ .

Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus.

Q-nexus is a software tool for ChIP-nexus data using the random barcodes used in the ChIP-nexus protocol to selectively remove duplicate polymerase chain reaction (PCR) products.

Q-nexus

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