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NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq…
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:
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