[maker-devel] CDS retrieve from augustus_masked

[Carson Holt]

Augustus only predicts UTR for a handful of organisms.  I trim them off the
rejected models before outputting to the GFF3 as match/match_part features
(per my previous e-mail concerning the limitations of GFF3).

 --Carson

From:  Michael Thon <mike.thon at gmail.com>
Date:  Saturday, 6 April, 2013 10:37 AM
To:  "Kang, Yang Jae" <kangyangjae at gmail.com>
Cc:  <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] CDS retrieve from augustus_masked

Thats a good point because 'transcripts' implies that it would have the
UTRs. Does augustus predict the UTRs?  I manually checked the translations
of the .transcript. file and I only found valid translations but that does
not mean that UTRs could not be present...
On Apr 6, 2013, at 1:24 PM, "Kang, Yang Jae" <kangyangjae at gmail.com> wrote:

> Thank for your quick response Mike
> I looked the file named transcript, but it might include UTRs I suspect. What
> I want to do is calculating Ka Ks values so that I need coding sequences. Is
> there any indication where is exact START and STOP in the transcript file?
>  
> Thank you
>  
>  
> From: Michael Thon [mailto:mike.thon at gmail.com <http://gmail.com> ]
> Sent: Saturday, April 06, 2013 8:20 PM
> To: Kang, Yang Jae
> Cc: maker-devel at yandell-lab.org
> Subject: Re: [maker-devel] CDS retrieve from augustus_masked
>  
> Hi Kang - After running fasta_merge there should be a file:
>  
> [prefix].all.maker.augustus_masked.transcripts.fasta
>  
> in the output directory.  Is that what you need?
> Mike
>  
> On Apr 6, 2013, at 9:25 AM, "Kang, Yang Jae" <kangyangjae at gmail.com> wrote:
> 
> 
> Dear everyone!
>  
> I want to retrieve CDS sequences from the output of maker; however, in the
> augustus_masked feature there is no indication of CDS or Exon like maker
> features. Is there any way for me to retrieve CDS from augustus_masked? There
> were protein sequences in outdir but no CDS information.
>  
> Thank you!
>  
> Kang, Yang Jae
> Ph.D.
> Cropgenomics Lab.
> College of Agriculture and Life Science
> Seoul National University
> Korea
>  
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