[maker-devel] Incorporating cufflinks in maker

[Jason Stajich]

I also echo this - also has anyone given BRAKER a try as an alternative
gene prediction input from augustus with hints through MAKER?
http://bioinf.uni-greifswald.de/augustus/downloads/


Jason Stajich
jason.stajich at gmail.com

On Thu, Apr 2, 2015 at 10:36 AM, Carson Holt <carsonhh at gmail.com> wrote:

> I actually find it better to process data with Trinity.  Cufflinks results
> tend to be too noisy, and any sensitivity lost by using an assembly
> approach instead of an alignment based approach is generally rescued by
> protein data.
>
> —Carson
>
>
> > On Mar 30, 2015, at 12:12 AM, Holmer, Rens <rens.holmer at wur.nl> wrote:
> >
> > Hi maker team,
> >
> > I am currently working on a project where we want to incorporate quite a
> lot of RNA-seq into our annotation. Currently I see two options:
> >
> > Provide the cufflinks output as EST-gff
> > Process cufflinks output with TransDecoder (find ORFs, annotate UTR,
> etc) and provide this as either pred_gff or model_gff
> >
> > What would you suggest, and what would be the required formatting for
> both options?
> >
> > Thanks in advance,
> >
> > Rens Holmer
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>
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