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RseqFlow is an RNA-Seq analysis pipeline which offers an express implementation of analysis steps for RNA sequencing datasets. It can perform pre and post mapping quality control (QC) for sequencing data, calculate expression levels for uniquely mapped reads, identify differentially expressed genes, and convert file formats for ease of visualization. A detailed description of the pipeline] is given here: https://sourceforge.net/p/rseqflow/wiki/PipelineDescription
RseqFlow offers two run mode options, a VM workflow managed with Pegasus and a unix run mode. See: https://sourceforge.net/p/rseqflow/wiki/TwoRunningModes
