[maker-devel] CDS file?

[Shane Brubaker]

Got it, thanks for your help!
________________________________________
From: Carson Holt [carsonhh at gmail.com]
Sent: Tuesday, July 31, 2012 10:58 AM
To: Shane Brubaker; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] CDS file?

Not really, but the functional annotation tools included with maker might be useful for some of the downstream work.  Although I guess there is a way I could fool maker's direct protein2genome gene creation into generating gene models with a little code modification.

--Carson


From: Shane Brubaker <sbrubaker at solazyme.com<mailto:sbrubaker at solazyme.com>>
Date: Tuesday, 31 July, 2012 1:17 PM
To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>, "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] CDS file?

One more question – do people ever run MAKER on transcriptomes?

From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Tuesday, July 31, 2012 6:01 AM
To: Shane Brubaker; maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] CDS file?

Use the fasta_tool script that comes with MAKER together with the --trim_maker_utr option.

Thanks,
Carson



From: Shane Brubaker <sbrubaker at solazyme.com<mailto:sbrubaker at solazyme.com>>
Date: Monday, 30 July, 2012 7:52 PM
To: "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: [maker-devel] CDS file?

Hi, does anyone know if maker outputs a file of just the CDS portion of transcripts?  I want to use it to determine a codon usage table.

Thanks,
Shane
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