ChIP-seq Visualization: IGV, UCSC Browser & deepTools Tutorial

Transform ChIP-seq peaks into interpretable visualizations using IGV, UCSC Genome Browser, and deepTools. Learn to create BED/BigWig files, load data in genome browsers, and generate publication-quality heatmaps and profile plots. 📚 FULL TUTORIAL WITH CODE: https://ngs101.com/how-to-analyze-chi... ⏱️ TIMESTAMPS: 0:00 - Tools for ChIP-seq Peak Visualization: IGV, UCSC & deepTools 1:10 - Format Peak Files: Convert to BED, BigWig & BigBed 4:24 - Visualize Peaks in IGV: Load Files & Navigate Genome 6:15 - Visualize Peaks in UCSC Genome Browser: Custom Tracks 8:36 - Visualize Peaks with deepTools: Heatmaps & Profile Plots 🔬 WHAT YOU'LL LEARN: ✅ Convert HOMER peaks to BED format with pos2bed.pl ✅ Create BigWig signal tracks using HOMER and deepTools ✅ Generate indexed BigBed files with bedToBigBed ✅ Load and navigate ChIP-seq data in IGV desktop application ✅ Create custom tracks in UCSC Genome Browser ✅ Generate heatmaps showing binding patterns with computeMatrix ✅ Create profile plots for average signal distribution ✅ Visualize TSS enrichment across gene promoters ✅ Compare ChIP vs Input signal tracks 🧬 KEY VISUALIZATION FORMATS: BED files: Discrete peak locations (chr, start, end) BigWig files: Continuous signal tracks (binding intensity) BigBed files: Indexed peaks for browser display BAM files: Aligned reads for detailed inspection Normalization: RPKM, TMM methods for fair comparison ⚠️ CRITICAL VISUALIZATION STEPS: File hosting: UCSC requires publicly accessible URLs (use Cyverse) Chromosome naming: Ensure consistency (chr1 vs 1) Signal scaling: Use consistent y-axis for sample comparison Resolution: 10bp bins balance detail and file size Color schemes: Blue for ChIP, gray for Input, intuitive palettes 🛠️ COMPLETE WORKFLOW: pos2bed.pl (BED) → bedToBigBed (BigBed) → bamCoverage/makeUCSCfile (BigWig) → IGV/UCSC (browse) → computeMatrix → plotHeatmap/plotProfile (publication figures) 📁 VISUALIZATION OUTPUTS: Interactive genome browser sessions (IGV, UCSC) Heatmaps sorted by signal intensity (PNG, PDF) Profile plots showing average binding patterns TSS enrichment plots around transcription start sites Multi-track comparisons (ChIP, Input, annotations) 🔔 Subscribe: @NGS101-LearningHub 📧 https://ngs101.com #ChIPseq #Visualization #IGV #UCSCBrowser #deepTools #Heatmap #GenomeBrowser #BigWig