Two similarly named packages
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. “Basic modules” quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while “RNA-seq specific modules” investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation
See more at http://code.google.com/p/rseqc/
RNA-SeqQC 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.
RNA-SeQC is built on the GATK as well as the Picard API.
See more at https://confluence.broadinstitute.org/display/CGATools/RNA-SeQC
Both tools are quite good and useful, however there are currently some novel applications available, which provide additional important quality control checks. For example, Qualimap is an open-source Java program, which includes several modes to analyze QC of high throughput sequencing alignment data. Two modes: RNA-seq QC and Counts QC are focused on analysis of RNA-sequencing data. The second version supports multi-sample quality control. There is a manuscript comparing the tool in detail to other packages.