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

Some environment variables need to be set appropriately before running any RSeQC scripts. This is most easily done by using the modules commands as in the example below:

biowulf% module avail rseqc

-------------- /usr/local/Modules/3.2.9/modulefiles -----------------------
rseqc/2.3
biowulf% module load rseqc

biowulf% module list
Currently Loaded Modulefiles:
  1) rseqc/2.3

Sample session

helix% module load rseqc

helix% bam_stat.py -i myfile.bam

helix% read_NVC.py -i myfile.bam -o nuc_comp -x
      
helix% overlay_bigwig.py -i bigwigfile1 -j bigwigfile2 -a Average -o out.wig

http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html