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Overview

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

Exciting Updates and Latest News

Keeping you up-to-date with the latest in NGS, Bioinformatics Analysis, and cancer genomics with blogs on Array Suite, OncoLand (TCGA and more), ImmunoLand, and more.

Filtering by Tag: Genome Browser

[Array Studio Analysis] Genome Browser Advanced Analysis of Variants, Fusion and Isoform Expression

Vivian Zhang

Besides basic navigation, visualization and annotation of genome sequence, the Omicsoft Genome Browser also enable users to perform advanced analysis on sequence variants, fusions, isoform expression, and copy number variation data. In this blog, we will introduce Genome Browser Advanced Analysis of Variants, Fusion and Isoform Expression.

Advanced Analysis of Variants, Fusion, and Isoform Expression

 

1 Annotate the Genome Browser with Sequence Variant Information

The Omicsoft Genome Browser can display sequence variants from your .BAM files. You can directly add annotation tracks from .vcf files, or even load .vcf files from Genomemark to quickly navigate your variants of interest.

Variant information and aligned read sequence in .bam coverage track.

Variant information and aligned read sequence in .bam coverage track.

 

2 View Gene Fusion Data in the Genome Browser

The Array Studio Fusion Mapping method identifies putative gene fusion events in DNA-seq and RNA-seq data, outputting both a Fusion Report and a set of .bam files containing only fusion-mapped reads. These reads can be viewed in the Genome Browser, and you can go directly from the Fusion Report to the Genome Browser to view both ends of the fusion in split-pane.  

Fusion tracks for example fusion ID FUS_526235345_526249828(++)

Fusion tracks for example fusion ID FUS_526235345_526249828(++)

 

3 Compare Sample-group Isoform Usage in the Genome Browser

Specific gene isoforms may play an important role in certain body functions. You can use Differentially Expressed Isoforms module in Analysis tab to identify interesting isoforms. In the Genome Browser, you can display relative transcript usage between sample groups to visualize and confirm reports of differential transcript usage.

Example of relative transcript usage between lung and skin tissues. As we can see, transcript us003lvs4 is highly expressed in skin tissue, which is in purple. The other transcript is mainly expressed in lung tissue, which is in blue.

Example of relative transcript usage between lung and skin tissues. As we can see, transcript us003lvs4 is highly expressed in skin tissue, which is in purple. The other transcript is mainly expressed in lung tissue, which is in blue.

 

4 Integrate CNV chip and DNA-seq Visualizations in the Omicsoft Genome Browser

Omicsoft Genome Browser allows user to visualize copy number variation (CNV) data. You can integrate DNA-Seq .bam coverage, SNP chip intensity and segmented CNV calls data for visualization. Please refer to DNA-Seq and copy number variation analysis tutorial to learn how to obtain and generate the data: DNA-seq pipeline .bam and segmented CNV calls, SNP chip intensity and segmented CNV calls.

Copy number variation data from DNA-Seq and SNP array datasets.

Copy number variation data from DNA-Seq and SNP array datasets.

Omicsoft Genome Browser has hundreds of features or options available. The best way to quickly learn to utilize our genome browser is to refer to our short video tutorial clips. Again, please check out our tutorial Genome Browser Advanced Analysis of Variants, Fusion and Isoform Expression.

[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.

[New Feature] Exon Junction Curve in Genome Browser to Show Exon Junction Curves Side by Side with Coverage

Vivian Zhang

Alternative Splicing (AS) is a process that exons or noncoding regions within DNA are differentially skipped or joined, resulting in different protein isoforms. This process allows individual genes to encode different mRNAs that encode proteins with diverse and even opposite functions. Alternative splicing has been shown to play an important role in a number of human diseases, including cancer, cardiovascular and neurodegenerative diseases. In Omicsoft Array Studio and Land, we provide modules and visualization functions that make it easier for users to research splicing. One example is the recent implemented function, Show Exon Junction Curve in Omicsoft Genome Browser.

Previously, in Omicsoft Genome Browser, we provide Exon Junction information in each individual track: 

Lung adenocarcinoma sample RNA-Seq data in Genome Browser. The blue lines below the read signal and the numbers indicate the number of exon junction reads. 

Lung adenocarcinoma sample RNA-Seq data in Genome Browser. The blue lines below the read signal and the numbers indicate the number of exon junction reads. 

The Show Exon Junction function allows user to checkout the number of exon junction reads. To better improve the visualization especially in the case of alternative splicing, we implemented Exon Junction Curve function:

Lung adenocarcinoma sample RNA-Seq data in Genome Browser with Exon Junction Curves. The LUAD track represents all lung adenocarcinoma samples. The Solid Tissue Normal and Primary Tumor tracks represent the normal and tumor sample from lung adenocarcinoma subject respectively. 

Lung adenocarcinoma sample RNA-Seq data in Genome Browser with Exon Junction Curves. The LUAD track represents all lung adenocarcinoma samples. The Solid Tissue Normal and Primary Tumor tracks represent the normal and tumor sample from lung adenocarcinoma subject respectively. 

Exon Junction Curve provides better visualization of exon junction events. In above example, it clearly shows the alternative splicing in lung adenocarcinoma samples (Two curves in LUAD track). The height of the curve represents the number of reads scaled to the total reads within the same track. In contrast,  the Solid Tissue Normal and Primary Tumor tracks only have one exon junction curve for each track, implying that differential splicing of PMP22 occurs in tumor and normal samples. 

 

 

[Feature Review] Add Virtual Genome File from HTTP to Genome Browser

Vivian Zhang

The increasing number of available public datasets, such as from the National Cancer Institute (NCI), Gene Expression Omnibus (GEO), Catalogue of somatic mutations in cancer (COSMIC) and The Encyclopedia of DNA Elements (ENCODE) Consortium, makes it much easier for researchers to conduct biomedical and clinical research.

Want to check a sample’s genome for mutations or gene expression? There could be VCF, BigWig files and BAM files available from a variety of sources.

The number of studies based on whole genome sequencing is skyrocketing, due to the development of Next Generation Sequencing technology that has decreased sequencing costs. However, with the large sequencing files, especially publicly available BAM files public, downloading these file takes hours or even days.

In Array Studio, Genome Browser allows users to Add Track from URL:

This allows users to add sorted BAM files, sorted VCF files, BAS files, BigBed and BigWig files and more from the URL. Once added, the Genome Browser only takes a few seconds to load. 
For more details, please read our wiki page: http://www.arrayserver.com/wiki/index.php?title=Add_GenomeBrowser_Track_From_URL


If you are an OncoLand user, you may want to check out your sample of interest in the Land. We already downloaded and preprocessed thousands of samples, and included source files for most RNA-Seq data that are genome browser-ready. If you are not a Land user, contact us for a free demo!

Array Studio and Land: integral in helping you save time and accelerate your research discovery.