RNA-Seq – Understanding transcript expression and finding novel variants
The interpretation of RNA-Seq data requires accurate, comprehensive annotation. This is now more true than ever, as sequencing delivers unbiased coverage with ever increasing read quality and depth. To take full advantage of this, Genomatix provides a comprehensive promoter and transcript annotation database. In addition, a substantial literature annotation database (expert and automated curation) is used to generate regulatory networks and interpret novel findings in light of previous publications.
For mapping the RNA-Seq reads Genomatix supports multiple libraries (mapping references) each tailored for a specific analysis. To obtain gene/transcript coverages and normalized expression values the transcriptome library is used. To get information on novel splice-junctions reads are mapped to the splice-junction library. For finding novel exons and transcripts the genome library can be used. When mapping to the genome we support multi-spliced alignments with additional splice-signal detection.
It has always been a strength of Genomatix to provide powerful tools for the downstream analysis of high throughput data - to get to the biology behind it. For RNA-Seq the following tools are of particular interest: gene fusion detection, alternative splicing analysis, gene regulatory networks, signaling pathways and networks (GePS), gene enrichments, differential expression and a large body of literature annotations supporting each finding.