transcript assembly of RNA-seq data

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transcript assembly of RNA-seq data

Quanwei Zhang
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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Re: transcript assembly of RNA-seq data

Carson Holt-2
(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 <[hidden email]> 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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maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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Re: 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 <[hidden email]> on behalf of Carson Holt <[hidden email]>
Date: Friday, January 27, 2017 at 10:23 AM
To: Quanwei Zhang <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
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 <[hidden email]> 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
 
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




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Re: transcript assembly of RNA-seq data

Carson Holt-2
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 <[hidden email]> 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 <[hidden email]> on behalf of Carson Holt <[hidden email]>
Date: Friday, January 27, 2017 at 10:23 AM
To: Quanwei Zhang <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
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 <[hidden email]> 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
 
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





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[hidden email]
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