Overview
The IGV (Integrative Genomics Viewer) in Expressions provides an interactive platform for visualizing sequencing alignments, coverage plots, and genomic variations. This tool allows users to analyze sample data within a genomic context while maintaining intuitive navigation and customization options.
Getting started
Selecting samples for visualization
- The Sample Basket (left panel) lists selected samples.
- Click Visualize to load these samples into the Genome Browser.
- The genome browser will display coverage plots (BigWig), read alignments (BAM), and variant information (VCF).
Navigating the Genome Browser
- Genome & Chromosome selection
- Choose the reference genome (e.g., hg38) from the drop-down menu.
- Choose the chosen chromosome of interest or enter specific chromosomal coordinates/gene name to zoom into a particular region.
- Navigation tools
- Zoom In/Out to refine your view.
- Pan left/right across the region.
- Track labels toggle allows sample names to be displayed or hidden.
- Select Tracks enables adding or removing specific data tracks for comparison.
Understanding read alignments & variants
- Reads appear as gray bars, representing sequencing alignments.
- Colored sections:
- Blue = reference allele
- Red = alternate allele
- Gray regions = Sections same as reference genome.
- Coverage plots above the reads indicate sequencing depth across genomic regions.
Exporting & Saving Data
- Click Save Image to export the genome view as a high-resolution image.