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Omicsoft is the leading provider of Next Generation Sequencing, Cancer Genomics, Immunology, and Bioinformatics solutions for Next Generation Sequencing Data and Gene Expression Analysis.

[Array Studio Analysis] Getting Started with Genome Browser: Basic navigation, visualization and annotation

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[Array Studio Analysis] Getting Started with Genome Browser: Basic navigation, visualization and annotation

Vivian Zhang

Omicsoft Genome Browser is a fully-featured genomic data visualization interface. It is fully integrated with Array Suite (Array Viewer, Array Server and Array Studio). Omicsoft Genome Browser empowers Array Suite's visualization capacity on a variety of different genomic data types with hundreds of functions and features. In this blog, we are glad to introduce our video tutorial: Getting Started with the Genome Browser. Starting from the most basic features, we present to you how to navigate, visualize and annotate your genomic data.

1 Getting Started with the Omicsoft Genome Browser

1.1 Basic Navigation in the Genome Browser

Omicsoft's Genome Browser has a very user-friendly user interface with powerful features. Navigation toolbar provides a variety of navigation features, from searching gene, transcript or sequence to jumping through genome region, adjusting, from zooming in/out to hiding, splitting or saving views. By bookmarking to Genomemark, queried genome region will be bookmarked for future usage. Track properties window allows user to fine-tune track display. 

Example Genome Browser interface.

Example Genome Browser interface.

Some of the very basic features introduced in the video tutorial include:

  • Bookmark custom genomic regions 
  • Trim introns to view only exon data 
  • Search by nucleotide sequence 
  • Retrieve DNA, RNA, or protein sequence for a region or feature 
  • Modify track display details
  • Save and share your browser session 
  • Add annotation tracks 

 

1.2 Add .bam Alignment Files to View Genome Coverage

Omicsoft Genome Browser provides multiple options to add tracks. Users can add .bam file to Genome Browser to view genome coverage. Even if you are not sure of your reference genome, you can use BAM Tools | Extract header and refer reference library ID to refer it. Next, simply Add Track From Local File or Server File

Refer reference library ID and add .bam file from server file

Refer reference library ID and add .bam file from server file

 

1.3 Add .bam Alignment Data from Array Studio Analysis

Alternatively, if you have files saved in Analysis project already, you can also right click on data object to create new genome browser, and Add Track from Analysis in Genome Browser.

Add Track from Analysis. Select the data you just created new genome browser in Analysis tab.

Add Track from Analysis. Select the data you just created new genome browser in Analysis tab.

1.4 Advanced Visualization of .bam Alignment Information

BAM alignment files contain nucleotide-level genome coverage, read quality, exon-junction, and sequence variant information. You can directly view all of this information in the Omicsoft Genome Browser. Example queries include:

  • Display exon junction information 
  • Interpreting exon junction information 
  • View the Alignment Profile of your .bam data 
  • Filter reads based on mapping metrics 
  • Display read pair connections
  • Filter displayed reads by quality 
  • View sequence variant data 
  • View nucleotide-level quality information 
Exon Junction Curve marks exon junction positions.

Exon Junction Curve marks exon junction positions.

Exon Junction Details indicates the orientation and the number of sequence mapped to exon junction positions.

Exon Junction Details indicates the orientation and the number of sequence mapped to exon junction positions.

Alignment Profile displays aligned sequence.

Alignment Profile displays aligned sequence.

Show Variant displays variant loci and mutation frequency.

Show Variant displays variant loci and mutation frequency.

2 Annotating Genomic Features and Coverage

The Omicsoft Genome Browser provides several ways to annotate genome features and visualize genome coverage, as well as splicing, read quality, and variation. For example, you can annotate ChIP peak locations and regulatory regions from Browser-Extensible Data (BED) files. Omicsoft provides many popular annotation tracks, or you can add your own. If you created .bedgraph files for viewing NGS coverage in other genome browsers, you can quickly load these into the Omicsoft Genome Browser. BAM Summary (BAS) files retain coverage, exon junction, and sequence variant information from BAM files, but can be up to 63x smaller. 

To learn how to navigate these files and tracks, please check out our tutorial video 2 Annotating Genomic Features and Coverage for details.