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

ABSTRACT:

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

SUBMITTER: Hansen P 

PROVIDER: S-EPMC5097360 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature