Hello,

I am reading the STAR manual and I came across the publication for STAR-fusion. I could not understand how different they are from each other. Could someone help me understand the difference?

Thank you in advance. 
STAR aligner is a splice aware aligner that aligns junction reads using a guide GTF. [STAR-fusion][1] allows identification of [fusion transcripts][2]. In many cases you get fusion transcripts due to chromosomal translocation (cancer) or trans-splicing etc. Other splice aware aligners ([Tophat-Fusion][3]) also have fusion engine for same purpose.


  [1]: https://github.com/STAR-Fusion/STAR-Fusion/wiki
  [2]: https://en.wikipedia.org/wiki/Fusion_transcript
  [3]: http://ccb.jhu.edu/software/tophat/fusion_index.shtml