DamMapper

DamMapper analyzes DamID-seq data through a Snakemake workflow that processes multiple biological replicates with quality control visualization to map genome-wide chromatin-protein interactions.

Key Features:

• Replicate Processing: The workflow processes multiple biological replicates.
• Quality Control Visualization: Generates correlation heatmaps and principal component analysis (PCA).
• Reproducibility: Ensures reproducibility across diverse computational environments, including cloud computing and high-performance computing (HPC) clusters, through Conda software environments and Docker/Apptainer containerisation.
• Code Quality: Maintains robust code quality through continuous integration (CI).

Scientific Applications:

• Chromatin-Protein Interaction Mapping: Maps genome-wide chromatin-protein interactions using DamID-seq data.
• Transcription Factor Binding Analysis: Generates genome-wide DNA binding maps for transcription factors such as HIF-1α.
• Histone Methyltransferase Binding Analysis: Generates the first genome-wide DNA binding map for histone methyltransferases such as SET1B.
• Validation Against ChIP-seq: Enables comparison and validation of DamID-seq results against ChIP-seq data, as demonstrated by strong concordance between HIF-1α DamID-seq and ChIP-seq results.
• Hypoxia Response Research: Facilitates analysis of proteins involved in the hypoxia response.

Methodology:

DamMapper is implemented using the Snakemake workflow management system with software environments managed by Conda and containerisation using Docker/Apptainer.