Currently available analysis tools are often not easily installed by the general biologist and most of them lack inherent parallel processing capabilities widely recognized as an essential feature of next-generation bioinformatics tools. Presented here is a user-friendly and fully automated RNA-Seq analysis pipeline (R-SAP) with built-in multi-threading capability to analyze and quantitate high-throughput RNA-Seq datasets. R-SAP follows a hierarchical decision making procedure to accurately characterize various classes of transcripts and achieves a near linear decrease in data processing time as a result of increased multi-threading. In addition, RNA expression level estimates obtained using R-SAP display high concordance with levels measured by microarrays.
R-SAP program is publicly available at www.mcdonaldlab.biology.gatech.edu/r-sap.htm.
- Mittal VK, McDonald JF. (2012) R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data. Nucleic Acids Res [Epub ahead of print]. [article]