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evidence of transcript assembly

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evidence of transcript assembly

Quanwei Zhang
Hello:

I am using Maker2 to do gene annotation on a new rodent species. I have found some published RNA-seq data and there are selected open reading frames. Generally they get the transcript assembly through Trinity, after that they mapped the raw  transcript assemblies to mouse genome and selected those with full coverage of mouse genes or part coverage. I have a questions about the evidence of transcript assembly for Marker. Which do you think is a best choice as evidences to Maker2?
(1) All the Trinity transcript assemblies?
(2) Trinity transcript assemblies that fully cover the mouse genes?
(3) Trinity transcript assemblies either fully or partly cover the mouse genes?

Many thanks

Best
Quanwei

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Re: evidence of transcript assembly

Carson Holt-2
Different sources of data will have different levels of quality. You may want to run them all, then look at results in a browser like Apollo. If specific source look like they are more problematic than others, then drop them.

—Carson



> On Mar 20, 2017, at 11:09 AM, Quanwei Zhang <[hidden email]> wrote:
>
> Hello:
>
> I am using Maker2 to do gene annotation on a new rodent species. I have found some published RNA-seq data and there are selected open reading frames. Generally they get the transcript assembly through Trinity, after that they mapped the raw  transcript assemblies to mouse genome and selected those with full coverage of mouse genes or part coverage. I have a questions about the evidence of transcript assembly for Marker. Which do you think is a best choice as evidences to Maker2?
> (1) All the Trinity transcript assemblies?
> (2) Trinity transcript assemblies that fully cover the mouse genes?
> (3) Trinity transcript assemblies either fully or partly cover the mouse genes?
>
> Many thanks
>
> Best
> Quanwei
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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