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RNA-Seq has become one of the most important new approaches for gene expression analysis as well as transcriptome analysis. The issue of how to analysis RNA-Seq data is one of the biggest challenges for current transcriptomics research. In this study, we develop an RNA-Seq data annotation pipeline named RNADAP, which is an efficient transcriptomes analysis tool to evaluate gene expression quantization in isoform level and compatible for reads data from different platforms. RNADAP is a typical Java application so the pipeline could be carried out on Windows as well as Linux. The installation process is convenient and user can grasp it very easily with a friendly user interface. RNADAP is a free, open-source software and written in Java. All source code, instructions, testing data and additional scripts are available at http://rnadap.sourceforge.net/.