deepTools: NGS Data Analysis Toolkit

--- name: deeptools description: "NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization." --- # deepTools: NGS Data Analysis Toolkit ## Overview deepTools is a comprehensive suite of Python command-line tools designed for processing and analyzing high-throughput sequencing data. Use deepTools to perform quality control, normalize data, compare samples, and generate publication-quality visualizations for ChIP-seq, RNA-seq, ATAC-seq, MNase-seq, and other NGS experiments. **Core capabilities:** - Convert BAM alignments to normalized coverage tracks (bigWig/bedGraph) - Quality control assessment (fingerprint, correlation, coverage) - Sample comparison and correlation analysis - Heatmap and profile plot generation around genomic features - Enrichment analysis and peak region visualization ## When to Use This Skill This skill should be used when: - **File conversion**: "Convert