deeptools - Analyze and visualize NGS sequencing data
Processes BAM and related genomic files for coverage conversion, quality control, sample comparison, normalization, and visualization of NGS experiments.
Tags
Updated: 2026-10-04Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Convert BAM coverage tracks
- Assess sequencing quality
- Compare sequencing samples
- Normalize genomic signals
- Generate heatmaps and profiles
- Analyze enrichment at peaks
- Generate workflow scripts
- Validate input files
Inputs
- BAM files
- BAM indices
- bigWig files
- BED region files
- Genome assembly
- Effective genome size
- Analysis parameters
Outputs
- Normalized coverage tracks
- Comparison tracks
- Quality control plots
- Correlation and PCA plots
- Heatmaps and profile plots
- Enrichment visualizations
- Workflow scripts
- Input validation status
Requirements
- Python environment
- deepTools installation
- Command-line shell
- Readable input files
- Indexed BAM files for BAM analysis