deeptools

Topics in the source

• deepTools: NGS Data Analysis Toolkit
• Overview
• When to Use This Skill
• Quick Start
• 1. Validate Input Files
• 2. Generate Workflow Template
• 3. Most Common Operations
• Installation

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 This skill should be used when: File conversion: "Convert BAM to bigWig", "generate coverage tracks", "normalize ChIP-seq data" Quality control: "check ChIP quality", "compare replicates", "assess sequencing depth", "QC analysis" Visualization: "create heatmap around TSS", "plot ChIP signal", "visualize enrichment", "generate profile plot" Sample comparison: "compare treatment vs control", "correlate samples", "PCA analysis" Analysis workflows: "analyze ChIP-seq data", "RNA-seq coverage", "ATAC-seq analysis", "complete workflow" Working with specific file ty

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