This repository documents the analysis pipeline for an ATAC-seq experiment investigating chromatin accessibility changes across the genome in leukemia NPM1 mutant cells. The study compares three control groups (DMSO) and three experimental groups (dTAG).
The pipeline includes the following key steps:
- Quality Control (QC): Ensuring data quality and integrity for downstream analysis.
- Peak Calling: Identifying regions of open chromatin.
- Differential Accessibility Analysis: Determining genomic regions with significant changes in accessibility between groups.
- Annotation: Mapping identified peaks to genes and genomic features.
- QC Guide: ATACseqQC Bioconductor Vignette
- Pipeline Workflow: ATAC-seq Workshop by Sean Davis
- scripts: Code for data preprocessing, alignment, and analysis.
- results: Key findings, including peak files and visualizations.
Feel free to explore the repository and adapt the pipeline for your ATAC-seq projects!