Quick Start

In order to produce quality control metrics, plots, and pdf reports on a single replicate, simply use the command:

java -Xmx4G -jar /path/to/jarfile/QoRTs.jar QC \
                   --generatePlots  \
                   mybamfile.bam  \
                   transcriptAnnotationFile.gtf.gz  \
                   /qc/data/dir/path/

Note: This command must be executed as a single line. Additional options may be required depending on the nature of the dataset. For single-ended data, the --singleEnded option should be included. For strand-specific data, the --stranded option should be included, and possibly also the --fr_secondStrand option depending on the stranded library type. For position-sorted data, the --coordSorted option should be used. See 6, or the QC utility documentation⁵ for more information on the available options.