[maker-devel] CDS file?

[Carson Holt]

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>
Date:  Tuesday, 31 July, 2012 1:17 PM
To:  Carson Holt <carsonhh at gmail.com>, "maker-devel at yandell-lab.org"
<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
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>
Date: Monday, 30 July, 2012 7:52 PM
To: "maker-devel at yandell-lab.org" <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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