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

[Carson Holt]

No. My experience has just been with regular Trinity de novo assembly. Of course, I’d be interested in any one else’s attempt at this though.

—Carson


> On Jan 27, 2017, at 3:21 PM, Fields, Christopher J <cjfields at illinois.edu> wrote:
> 
> Yup I agree.  Carson, would you know of any instances where HiSAT2/STAR+Stringtie or reference-based Trinity assemblies were (successfully) used?  
> 
> chris
> 
> From: maker-devel <maker-devel-bounces at yandell-lab.org <mailto:maker-devel-bounces at yandell-lab.org>> on behalf of Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
> Date: Friday, January 27, 2017 at 10:23 AM
> To: Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>>
> Cc: "maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> Subject: Re: [maker-devel] transcript assembly of RNA-seq data
> 
>> (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 <mailto: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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>> 
> 
> 
> 

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