Does STAR identify new splicing?

Question

[zhangzhenyusz]

At beginning I was using Tophat-Cufflinks and had processed several sets of data. But it was way too slow so I switched to STAR. However, I found that output from STAR has much less number of isoform detected than Tophat-Cufflinks. Also the output from STAR seems to be all annotated. So I wonder if there is an option for STAR to identify new splicing sites.

Answer 1

[h.mon]

As this was very difficult to find (like googling for STAR novel splice), I will post it here so others can benefit. From (one of) STAR paper:

In addition to detecting annotated and novel splice junctions, STAR is capable of discovering more complex RNA sequence arrangements, such as chimeric and circular RNA.

P.S.: read section 8) 2-pass mapping from STAR manual.