A bioinformatic pipeline to analyze ChIP-exo datasets
Journal article, 2019

The decrease of sequencing cost in the recent years has made genome-wide studies of transcription factor (TF) binding through chromatin immunoprecipitation methods like ChIP-seq and chromatin immunoprecipitation with lambda exonuclease (ChIP-exo) more accessible to a broader group of users. Especially with ChIP-exo, it is now possible to map TF binding sites in more detail and with less noise than previously possible. These improvements came at the cost of making the analysis of the data more challenging, which is further complicated by the fact that to this date no complete pipeline is publicly available. Here we present a workflow developed specifically for ChIP-exo data and demonstrate its capabilities for data analysis. The pipeline, which is completely publicly available on GitHub, includes all necessary analytical steps to obtain a high confidence list of TF targets starting from raw sequencing reads. During the pipeline development, we emphasized the inclusion of different quality control measurements and we show how to use these so users can have confidence in their obtained results.

analytical pipeline

ChIP-exo

chromatin immunoprecipitation

Author

Christoph Sebastian Börlin

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

David Bergenholm

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Petter Holland

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Jens B Nielsen

Technical University of Denmark (DTU)

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

BioInnovation Institute

Biology Methods and Protocols

2396-8923 (ISSN)

Vol. 4 1 bpz011

Subject Categories

Other Computer and Information Science

Bioinformatics and Systems Biology

Genetics

DOI

10.1093/biomethods/bpz011

More information

Latest update

10/16/2020