BackgroundRNA-Seq technology is routinely used to characterize the transcriptome, and to detect gene expression differences among cell types, genotypes and conditions. Advances in short-read sequencing instruments such as Illumina Next-Seq have yielded easy-to-operate machines, with high throughput, at a lower price per base. However, processing this data requires bioinformatics expertise to tailor and execute specific solutions for each type of library preparation.ResultsIn order to enable fast and user-friendly data analysis, we developed an intuitive and scalable transcriptome pipeline that executes the full process, starting from cDNA sequences derived by RNA-Seq [Nat Rev Genet 10:57-63, 2009] and bulk MARS-Seq [Science 343:776-779, 2014] and ending with sets of differentially expressed genes. Output files are placed in structured folders, and results summaries are provided in rich and comprehensive reports, containing dozens of plots, tables and links.ConclusionOur User-friendly Transcriptome Analysis Pipeline (UTAP) is an open source, web-based intuitive platform available to the biomedical research community, enabling researchers to efficiently and accurately analyse transcriptome sequence data.

Let X be an algebraic curve. We study the problem of parametrizing geometric structures over X which are only generically defined. For example, parametrizing generically defined maps (rational maps) from X to a fixed target scheme Y . There are three methods for constructing functors of points for such moduli problems (all originally due to Drinfeld), and we show that the resulting functors are equivalent in the fppf Grothendieck topology. As an application, we obtain three presentations for the category of D-modules 'on' B(K)\G(A)/G(O), and we combine results about this category coming from the different presentations.

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