Question: How to find novel isoforms in RNA-Seq Data
1
gravatar for williamsbrian5064
7 months ago by
williamsbrian5064100 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 7 months ago by h.mon20k • written 7 months ago by williamsbrian5064100
4
gravatar for h.mon
7 months ago by
h.mon20k
Brazil
h.mon20k 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 7 months ago • written 7 months ago by h.mon20k
1

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

ADD REPLYlink written 7 months ago by Rob2.8k
1
gravatar for Buffo
7 months ago by
Buffo1.2k
Buffo1.2k wrote:

Try the new protocolo tuxedo

ADD COMMENTlink written 7 months ago by Buffo1.2k
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