want coding sequences

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want coding sequences

Quanwei Zhang
Hello:

Thanks for development and maintenance of the tool "Maker2".  We have used Maker2 to do genome annotation of a new rodent species. Now we are doing downstream analysis, which requires inputs of coding sequences from different species.

I found the outputs I got from Maker2 only include protein sequences and transcripts. Is there an easy way that I can get the coding sequences for our annotated genome?

Many thanks

Best
Quanwei

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Re: want coding sequences

Carson Holt-2
Use the fasta_tool utility with —trim_maker_utr to get just the CDS part of each transcript.

—Carson



> On May 10, 2017, at 9:48 AM, Quanwei Zhang <[hidden email]> wrote:
>
> Hello:
>
> Thanks for development and maintenance of the tool "Maker2".  We have used Maker2 to do genome annotation of a new rodent species. Now we are doing downstream analysis, which requires inputs of coding sequences from different species.
>
> I found the outputs I got from Maker2 only include protein sequences and transcripts. Is there an easy way that I can get the coding sequences for our annotated genome?
>
> 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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