This app implements selected packages from the RSeQC suite. These are:

• geneBody_coverage
• inner_distance
• junction_annotation
• read_distribution
• read_duplication

The app requires as input RNA-Seq mappings and a BED file describing the gene model used for or derived from these mappings.

Optionally, the user may estimate the amounts of different contaminants in the sample. This is done by suppling sequences through the "contaminants" input, which takes any number of ContigSet objects. FASTA files may be imported into ContigSet objects using the Genome Importer app.

One or more Reads objects MUST also be given if contaminants are given. The reads will be matched against each contaminant using the BWA app and the percent mapping will be stored.

The output is a set of charts in a report that can be viewed by selecting the report object in the data browser.