Getting Started with the Genome Browser
From Array Suite Wiki
Getting Started with the Omicsoft Genome Browser
The Omicsoft Genome Browser is a fully-featured interface to visualizing your genomic data. This video will explain the basics of getting around the genome, and some basic customization of the default annotation tracks.
- Create a new Browser session [00:30]
- Zoom in and out [01:20]
- Move to different genomic locations [01:45]
- Bookmark custom genomic regions [02:20]
- Trim introns to view only exon data [03:29]
- Search by nucleotide sequence [03:54]
- Retrieve DNA, RNA, or protein sequence for a region or feature [04:58]
- Modify track display details[05:15]
- Save and share your browser session [06:17]
- Add annotation tracks [06:48]
Add .bam Alignment Files to View Genome Coverage
The Omicsoft Genome Browser can directly load .bam files as coverage tracks, so you can immediately explore genome coverage and variation of your NGS data.
- Check that your .bam files match the Genome Browser reference genome [00:11]
- Sort your .bam files for the Genome Browser [01:20]
- Add new .bam files as separate tracks [01:43]
- Add new .bam files as a group [02:19]
- Separate/Merge grouped .bam files [02:54]
- Rename .bam group track [03:10]
- Rearrange genome coverage tracks [03:30]
Add .bam Alignment Data from Array Studio Analysis
While you can add .bam files directly to the Genome Browser, you can just as easily open .bam files that were added to an Array Studio project. When .bam files from a project are added, associated Design metadata can be used to dynamically group your coverage tracks.
- Advantages of loading .bam data from Array Studio Analysis [00:10]
- Open NGS data from Analysis projects [00:30]
- Group .bam data tracks by Design metadata [01:10]
- Separate and Merge grouped .bam data [01:25]
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.
- Display exon junction information [00:20]
- Interpreting exon junction information [01:05]
- View the Alignment Profile of your .bam data [01:30]
- Filter reads based on mapping metrics [02:10]
- Display read pair connections [02:45]
- Filter displayed reads by quality [03:47]
- View sequence variant data [04:18]
- View nucleotide-level quality information [05:25]
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.
Add an Annotation Track from BED Files
The Omicsoft Genome Browser can display a track of annotated genomic features, such as ChIP peak locations and regulatory regions, from Browser-Extensible Data (BED) files. Omicsoft provides many popular annotation tracks, or you can add your own. You can customize feature display by score and color information stored in the file.
- Add a new pre-configured .bed track [00:12]
- Color features by score [00:33]
- Add your own .bed file [00:45]
Add a Bedgraph File
If you created .bedgraph files for viewing NGS coverage in other genome browsers, you can quickly load these into the Omicsoft Genome Browser.
- Add a new bedgraph file[00:13]
- Customize track display properties[00:50]
Space-Efficient Visualization of Genome Coverage with BAS files
BAM Summary (BAS) files retain coverage, exon junction, and sequence variant information from BAM files, but can be up to 63x smaller. They are a great space-efficient alternative to bedgraph files for the Omicsoft Genome Browser.
- Advantages of .bas files over bedgraph files for Genome Coverage [00:10]
- Add a .bas file track [00:56]
- View exon junction and variation from .bas files [01:45]
- Freezing tracks to always display them [02:00]
Advanced Analysis of Variants, Fusion, and Isoform Expression
Annotate the Genome Browser with Sequence Variant Information
The Omicsoft Genome Browser can display sequence variants from your .BAM files. You can add annotation tracks from Sequence Variant Analysis .vcf output files. You can even load .vcf files as GenomeMark features for quick navigation to variants of interest.
- Add a .vcf file to annotate variants in your Genome Browser tracks [00:10]
- Add variant data as a GenomeMark [00:30]
- Browsing GenomeMark mutations [1:33]
- Display variant information in .bam/.bas coverage tracks [01:45]
- Display aligned reads in .bam coverage tracks [02:37]
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.
- Add fusion alignment reads to the Genome Browser [00:09]
- Freeze tracks to keep them visible [01:06]
- View and intepret Alignment Profile at fusions [01:26]
- View fusions directly from the Fusion Report [01:48]
- Filter reads for a specific fusion ID [02:27]
Compare Sample-group Isoform Usage in the Genome Browser
You can display relative transcript usage between sample groups in the Omicsoft Genome Browser, just like the Exon-Level Genome Browser View in Array Lands. With this schematic display, you can quickly confirm reports of differential transcript usage from the Differentially Expressed Isoforms module.
- Generate,find and copy transcript quantification .ngs2tex files to .bam folder [00:48]
- Check output folder and Gene Model of quantification data objects in "View Source" [01:14]
- Open a new Genome Browser containing grouped .bam coverage tracks [02:17]
- Display isoform usage on the transcript model [03:05]
- Visually check Differential Isoform Report results [04:10]
- Interpret isoform color and opacity regarding isoform usage [04:24]
Integrate CNV chip and DNA-seq Visualizations in the Omicsoft Genome Browser
After importing and segmenting your SNP chip and DNAseq (WXS/WGS) data into Array Studio, you can quickly visualize them in the Genome Browser. Array Studio Views can take you to a region of interest, or you can just explore.
- Source Data: DNA-seq pipeline .bam and segmented CNV calls, SNP chip intensity and segmented CNV calls [00:19]
- Open Genome Browser session on region of interest [01:18]
- Set .bam display track properties to compare coverage [02:17]
- Add SNP Array probe-level intensity data [02:50]
- Set SNP display track properties to compare intensities [03:29]
- Add Copy number predictions [04:15]
- Customize Copy number tracks [04:55]
- Choose a new region from Analysis to view with custom Genome Browser tracks [05:45]