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[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.