deepTools — NGS Data Analysis Toolkit

Overview

deepTools is a command-line toolkit for processing and visualizing high-throughput sequencing data. It converts BAM alignments to normalized coverage tracks (bigWig), performs quality control (correlation, PCA, fingerprint), and generates publication-quality heatmaps and profile plots around genomic features. Supports ChIP-seq, RNA-seq, ATAC-seq, and MNase-seq.

When to Use

• Converting BAM files to normalized bigWig coverage tracks
• Comparing ChIP-seq treatment vs input control (log2 ratio tracks)
• Assessing sample quality: replicate correlation, PCA, coverage depth
• Evaluating ChIP enrichment strength (fingerprint plots)
• Creating heatmaps and profile plots around TSS, peaks, or other genomic regions
• Analyzing ATAC-seq data with Tn5 offset correction
• Generating strand-specific RNA-seq coverage tracks
• For read alignment, use STAR, BWA, or bowtie2 instead
• For peak calling, use MACS2 or HOMER instead
• For BAM/VCF file manipulation, use pysam instead