RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files. The output consists of HTML reports and tab delimited files of metrics data. This program can be valuable for comparing sequencing quality across different samples or experiments to evaluate different experimental parameters. It can also be run on individual samples as a means of quality control before continuing with downstream analysis.

Availability and Restrictions


The following versions of RNA-SeQC are available on OSC clusters:

Version Owens
1.1.8 X*
* Current default version

You can use module spider rna-seqc to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.


RNA-SeQC is available to all OSC users. If you have any questions, please contact OSC Help.

Publisher/Vendor/Repository and License Type

The Broad Insitute, Open source


Usage on Owens


To configure your environment for use of RNA-SeQC, run the following command:  module load rna-seqc. The default version will be loaded. To select a particular RNA-SeQC version, use module load rna-seqc/version. For example, use module load rna-seqc/1.1.8 to load RNA-SeQC 1.1.8.


This software is a Java executable .jar file; thus, it is not possible to add to the PATH environment variable.

From module load rna-seqc, a new environment variable, RNA_SEQC, will be set. Thus, users can use the software by running the following command: java -jar $RNA_SEQC {other options}.

Further Reading

Fields of Science: