Uniquely Mapping Reads are overestimated

[Rohit-Satyam]

Hi Developers

I observe that the Uniquely mapping read percentage provided by rnaseqc is huge as compared to the "Uniquely mapped reads %" reported by STAR _Log.final files. Is your Unique Rate of Mapped number calculated differently? For Example

An exemplary output of STAR and rnaseqc of a sample is attached below:

batch2.zip