deeptools

SUMMARY

What it does

This Agent Skill provides a comprehensive suite of Python command-line tools for processing and analyzing high-throughput sequencing data, based on deepTools. It enables BAM to bigWig/bedGraph conversion, quality control (fingerprint, correlation, coverage), sample comparison, heatmap and profile plot generation around genomic features, and enrichment analysis. The skill includes helper scripts for file validation and workflow generation, and references for tools, workflows, normalization methods, and effective genome sizes. It is designed for ChIP-seq, RNA-seq, ATAC-seq, and other NGS experiments.