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How to find novel isoforms in RNA-Seq Data

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?

rna-seq assembly next-gen sequencing
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updated by h.mon h.mon • written by williamsbrian5064 williamsbrian5064

2 answers

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.

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written by h.mon h.mon

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

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written by Rob Rob

Try the new protocolo tuxedo

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written by Buffo Buffo

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