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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.

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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.

[Array Studio Video Tutorial] RNA-Seq Analysis Basic functions: Reads Quantification, Exon Junction and Gene Fusion Detection

Vivian Zhang

RNA-Seq has become one of the most popular methods in gene and transcript level genomic research. It could help quantify gene and transcript expression, identify sequence variants and detect gene, transcript or exon level genomic events. Array Studio provides a variety of functions powerful enough for small and large scale genomic research. In this article, we will introduce a few basic and the most commonly used functions, including sequence quantification, gene annotation, exon junction detection and gene fusion detection. 

 

 

ArrayStudio provides a number of modules and options for RNA-Seq quantification at gene, transcript, exon and exon junction levels. Both FPKM and Count tables can be generated. 

Example RNA-seq gene count table and its corresponding design table.

Example RNA-seq gene count table and its corresponding design table.

 

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 the Land products, we provide modules and visualization functions that make it easier for users to research splicing. In RNA-Seq analysis, besides gene and transcript counts, Array Studio can report exon junction counts as well. Results can be visualized in Omicsoft's Genome Browser.

Exon junction report and genome browser view.

Exon junction report and genome browser view.

Mutation data allows user to compare mutation frequencies and research individual variants. Users can run the  Summarize Variant Data module to annotate variants. Variants can be annotated in Mutation Reports or VCF files, and visualized directly in the Genome Browser.

Mutation annotation report and example genome browser view of variant V600E. 

Mutation annotation report and example genome browser view of variant V600E. 

 

 

Fusion genes can play an important role in cancer mutations that have multiple effects on a target gene. At Omicsoft, we provide a powerful fusion detection algorithm in FusionMap. FusionMap identifies unmapped reads that span multiple genomic locations, indicating possible gene fusion events:

Map Fusion Reads module will detect fusion genes from fusion junction-spanning reads which can characterize fusion genes at base pair resolution. This works with single end or paired end data. Combined Fusion Analysis will run fusion junction spanning + inter-transcript fusion read pairs detection at the same time. It detects fusion junction spanning reads from unmapped reads in BAM files, and detects inter-transcript fusion read pairs from singletons from BAM alignment entries. It will return a report showing potential fusion genes and counts for each fusion junction  Combined fusion analysis can only be run on paired-end data. 

Fusion report reports fusion count data with fusion annotation information attached. Fusion genome browser can display sequence information at base pair resolution. 

Fusion report reports fusion count data with fusion annotation information attached. Fusion genome browser can display sequence information at base pair resolution