[maker-devel] transcript assembly of RNA-seq data

[Carson Holt]

(1) De novo assembly without mapping to any genome assembly (like Trinity)

You get a lower false positive rate (TopHat+Cufflink is too noisy). And protein evidence will make up for any loss of sensitivity associated with the De novo assembly path. Make sure to us the jaccard_clip option  to reduce transcript merging in Trinity.

—Carson


> On Jan 27, 2017, at 9:13 AM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> Hello: 
> 
> I wonder which is the best way to make use of RNA-seq data for gene annotation of a new genome assembly. 
> (1) De novo assembly without mapping to any genome assembly (like Trinity)?
> (2) TopHat+Cufflink do mapping to the new genome assembly, that want to annotate?
> (3) TopHat+Cufflink do mapping to a close annotated genome (like mouse or human)?
> 
> Thanks
> 
> Best
> Quanwei
>  
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