Abstract
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.