qorts

The QoRTs software package is a fast, efficient, and portable multifunction toolkit designed to assist in the analysis, quality control, and data management of RNA-Seq datasets. Its primary function is to aid in the detection and identification of errors, biases, and artifacts produced by paired-end high-throughput RNA-Seq technology. In addition, it can produce count data designed for use with differential expression and differential exon usage tools, as well as individual-sample and/or group-summary genome track files suitable for use with the UCSC genome browser.