This pipeline analyzes RNA-Seq data by aligning it to a reference genome using the STAR aligner (Dobin et al, Bioinformatics 2012), then quantifies the reads based on a reference transcriptome. The pipeline also includes pre- and post- alignment QA/QC, as well as a post-quantification coverage report to assess the quality of data generated. The STAR aligner is one of the fastest and more sensitive aligners, however it is also a memory intensive. We suggest the server running Partek Flow has a minimum of 16 GB of RAM to use this pipeline. Requirements: 16 GB RAM or higher. Pipeline compatible with Partek Flow 3.0 or later.