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

[Fields, Christopher J]

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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