If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and its DOI (see above).
DamMapper is a containerized Snakemake pipeline for reproducible and scalable analysis of single/paired-end DamID short read Illumina data.
If you use DamMapper in your pubblication, please cite it as follows:
Wit, N., Bertlin, J., Hynes-Allen, A. et al. Mapping SET1B chromatin interactions with DamID using DamMapper, a comprehensive Snakemake workflow. BMC Genomics 26, 914 (2025). https://doi.org/10.1186/s12864-025-12075-x
Documentation of how to use DamMapper can be found at https://damid-seq.readthedocs.io/en/latest/.
- DamID
- DamID principle
- Experimental considerations
- Software requirements
- Conda/Mamba
- Snakemake
- Apptainer
- Snakefetch
- Usage
- Preparing raw sequencing data
- Sample meta data and analysis settings
- Configuration of Snakemake
- Dry-run of the analysis
- Visualization of the workflow
- Running the analysis
- Report of the results
- Archive of the analysis
- Output files
- Quality control
- Visualization of damid data
- Peak-related plots
- Citation
- Workflow
- Software used in workflow
- literature
- DamID
- Source code
- Reporting issues