The MNase-defined cistrome-Occupancy Analysis (MOA-seq) is a high-throughput, genome-wide approach designed to globally identify putative transcription factor (TF) binding sites in a single experiment with relatively high resolution. This method typically produces footprint regions smaller than 100 base pairs.
- Nextflow-based workflow: Automates the entire analysis process, from quality control of raw sequencing reads to motif discovery of putative TF-binding sites.
- Differential binding analysis: Includes an R script (with DiffBind package) to assess differences in MOA footprints between two experimental conditions (e.g., control vs. treatment).
- Reproducibility: Provides a unified and standardized pipeline, addressing the current lack of integrated solutions in the literature, where workflows are often fragmented across multiple custom scripts.
Existing MOA-seq analysis approaches are typically scattered across various bash scripts in different publications, making reproducibility and standardization challenging. This pipeline was developed to fill that gap by offering a comprehensive, reproducible, and user-friendly solution.
If you use MOAflow for your analysis, please cite it using the following doi: https://doi.org/10.64898/2026.03.26.713914
An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.