How to find novel isoforms in RNA-Seq Data

Question

[williamsbrian5064]

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?

Answer 1

[h.mon]

StringTie is the sucessor of Cufflinks. There are plenty of relatively recent programs, for example, KNIFE, BIISQ, or SparseIso.

P.S.: see a comprehensive list at Omicstools.

[Rob]

I'd add scallop to that list of recent methods as well.

Answer 2

[Buffo]

Try the new protocolo tuxedo