The pipeline will include the following key components: ReadsMap tools for alignment of RNA-Seq reads to genome, Fgenesh++R identification of alternative transcripts gene prediction tolls, and ExpLevel tool for measuring expression levels of predicted transcript isoforms.
When use please reference: Igor Seledtsov, Vladimir Molodtsov, Peter Kosarev, Victor Solovyev: Transomics pipeline - tools for analysis of RNASeq data. http://linux5.softberry.com/cgi-bin/berry/programs/Transomics
We build the gene identification with RNA-Seq data based on components of FGENESH++ gene finding pipeline (Salamov, Solovyev, 2000; Solovyev et al., 2006; Solovyev, 2007), which is known as one of the most a ccurate eukaryotic gene identification tool and has been used in annotation of a dozen new genomes.
ReadsMap provide information on splice sites and intron positions that forces modified version of Fgenesh++ to produce gene models that are supported by RNASeq data.
Fgenesh++R provides possibility to predict tissue specific gene variant or even produce alternatively spliced gene models. These models can be visualized in the ReadsMap Viewer.
Finally, Transomics pipeline includes a module to compute a relative abundance (expression level) of alternative transcripts generated from the same gene locus using a solution of a system of linear equations.