The current revolution in sequencing technologies allows us to obtain a much more detailed picture of transcriptomes via RNA-Sequencing. We have devel- oped the first integrative online platform, oqtans, for quantitatively analyzing RNA-Seq experiments. Our approach of providing a self-contained machine image with the accessible, transparent Galaxy framework [1] minimizes the risk of using a third-party web service for data analysis. These services often disappear a few years after publication and render results irreproducible [2]. With oqtans, bioinformatics becomes reproducible by providing analysis building blocks for a customized workflow of read mapping, transcript reconstruction and quantitation as well as differential expression analysis.