RNA-Seq

RNA-Seq stands to replace existing transcript profiling technologies as it measures all RNA in a sample, not just the RNA that can be probed for using traditional chips. GenomeQuest provides a powerful workflow that integrates best-of-breed open source technologies in a commercially supported environment to measure gene expression and to discover novel splice variants.

Core features:

  1. Mapping. GenomeQuest maps reads first to the transcriptome of the species in question; it then follows this with a genome correction step to ensure that properly aligned reads to the transcriptome can be uniquely mapped, driving accuracy to the gene counting.
  2. RPKMs. GenomeQuest computes RPKMs (gene expression values) for each gene measured using the Audic-Claverie method.
  3. Novel splice variants and exons. genomeQuest utilizes the TopHat algorithm to detect novel transcripts and exons.
  4. Annotation. All of the genes are heavily annotated by function, read count, and RPKM. All annotation is massively filterable.
  5. Arbitrary reference genome. GenomeQuest’s RNA-Seq workflow can run on any animal, plant, or microbial genome.
  6. Arbitrary numbers of replicates. The RNA-Seq workflow can run on one sample or on thousands.
  7. Visualization. The RNA-Seq workflow pushes data to a wide variety of other tools, from GeneSpring, to Expressionist, to Ingenuity, to your favorite gene browser, to Excel, GeneGo, or virtually any other tool.

Also, researchers can immediately share the results with colleagues. All this comprehensive functionality is delivered in an easy-to-use environment from a web browser.

RNA-SEQ

RNA-Seq Interface


RNA-SEQ

RNA-Seq Interface



GenomeQuest Applications

All GenomeQuest science applications are delivered in an easy-to-use, integrated environment. They package all bioinformatics details – including read and reference data, scientific algorithms, all third party integration, all parameters, and the compute environment – into a simple form-based interface. Users query results using an interactive sequence browser. All data, parameters, and results can be shared with colleagues and teams using the GenomeQuest collaborative environment.

GenomeQuest applications are built to scale to thousands of samples, each with billions of reads. They support all popular sequencing machines (including Illumina, SOLiD, 454, and PacBio) and all common formats (including FASTQ, FASTA, SAM/BAM, VCF, SVA, and others).

Details on the Wiki