I was wondering if anyone knew of new software that can help find novel genes and isoforms from my RNA-seq data? I know there Cufflinks and what not but that is a bit old. I was wondering if anyone knew of anything newer? A lot of the genes in the genome that I am working with are predicted. I was interested to see if the RNA data matched up with the gene prediction? 
[StringTie][1] is the sucessor of Cufflinks. There are plenty of relatively recent programs, for example, [KNIFE][2], [BIISQ][3], or [SparseIso][4].

P.S.: see a comprehensive list at [Omicstools][5].


  [1]: https://ccb.jhu.edu/software/stringtie/
  [2]: https://github.com/lindaszabo/KNIFE
  [3]: https://github.com/bee-hive/BIISQ
  [4]: https://github.com/henryxushi/SparseIso
  [5]: https://omictools.com/novel-transcript-quantification-category