RseQC

RseQC is a high-throughput sequencing data processing tool specialized in RNAseq data.

Here is the link to the article presenting the tool.

It was developed by Liguo Wang, Wei Li and Shengqin Wang.

For RNA-seq data, RseQC is used in part 5, statistics. It will give various transcript and read statistics.

Figure 1 : simplified RNAseq pipeline.