Visualize: Genome Browser

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.