[maker-devel] Incorporating cufflinks in maker

[Carson Holt]

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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