Requirements

Hardware: The java utility performs the bulk of the data processing, and will generally require at least 4gb of RAM. In general at least 8gb is recommended if available. The R package is only responsible for some light data processing and for plotting/visualization, and thus has much lower resource requirements. It should run adequately on any reasonably-powerful workstation.

Software: The QoRTs software package requires http://www.r-project.org/R version 3.0.2 or higher, as well as https://www.java.comjava 6 or higher. It is strongly recommended that a 64-bit version of java be used, as the 32-bit versions generally cannot allocate sufficient RAM.

Annotation: QoRTs requires transcript annotations in the form of a gtf file. If you are using a annotation-guided aligner (which is STRONGLY recommended) it is likely you already have a transcript gtf file for your reference genome. We recommend you use the same annotation gtf for alignment, QC, and downstream analysis. We have found the Ensembl "Gene Sets" gtf³ suitable for these purposes. However, any format that adheres to the gtf file specification⁴ will work.

Dataset: QoRTs requires aligned RNA-Seq data. Data can be paired-end or single-end, unstranded or stranded (using either strandedness rule, see Section 7). It is strongly recommended, but not explicitly required, that the SAM/BAM files be sorted (either by name or position). QoRTs can use additional metadata (such as technical replicate status, case/control status, batch id, etc) to produce comparisons between these replicate groups, but this information is optional.