Question: How to find novel isoforms in RNA-Seq Data
1
gravatar for williamsbrian5064
2.6 years ago by
williamsbrian5064260 wrote:

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?

ADD COMMENTlink modified 2.6 years ago by h.mon31k • written 2.6 years ago by williamsbrian5064260
4
gravatar for h.mon
2.6 years ago by
h.mon31k
Brazil
h.mon31k wrote:

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.

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by h.mon31k
1

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

ADD REPLYlink written 2.6 years ago by Rob4.1k
1
gravatar for Buffo
2.6 years ago by
Buffo1.8k
Buffo1.8k wrote:

Try the new protocolo tuxedo

ADD COMMENTlink written 2.6 years ago by Buffo1.8k
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