How to find novel isoforms in RNA-Seq Data
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4.2 years ago

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 • 2.5k views
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4.2 years ago
h.mon 34k

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

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4.2 years ago
Buffo ★ 1.9k

Try the new protocolo tuxedo

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