ChEAP: ChIP-exo analysis pipeline and the investigation of Escherichia coli RpoN protein-DNA interactions.Genome-scale studies of the bacterial regulatory network have been leveraged by declining sequencing cost and advances in ChIP (chromatin immunoprecipitation) methods.  In this paper, we developed ChIP-exo Analysis Pipeline (ChEAP) that executes the one-step process, starting from trimming and aligning raw sequencing reads to visualization of ChIP-exo results.  The utility of ChEAP was demonstrated with the ChIP-exo datasets of RpoN sigma factor in E. coli K-12 MG1655.  To analyze two raw data files, ChEAP runtime was 2 min and 25 s.  ChEAP application in ChIP-exo data analysis is extensive and flexible for the parallel processing of data from various organisms.
ChEAP
ChEAP: ChIP-exo analysis pipeline and the investigation of Escherichia coli RpoN protein-DNA interactions.Genome-scale studies of the bacterial regulatory network have been leveraged by declining sequencing cost and advances in ChIP (chromatin immunoprecipitation) methods.  In this paper, we developed ChIP-exo Analysis Pipeline (ChEAP) that executes the one-step process, starting from trimming and aligning raw sequencing reads to visualization of ChIP-exo results. 
ChIP-exo Analysis Pipeline
The pipeline was implemented on the interactive web-based Python development environment - Jupyter Notebook, which is compatible with the Google Colab cloud platform to facilitate the sharing of codes and collaboration among researchers. 
Jupyter Notebook
The pipeline was implemented on the interactive web-based Python development environment - Jupyter Notebook, which is compatible with the Google Colab cloud platform to facilitate the sharing of codes and collaboration among researchers. 
Google Colab cloud platform