[maker-devel] CDS retrieve from augustus_masked

[Carson Holt]

I additionally found the offset value some position after Œ>¹ letter. Is
that indicate the starting ATG?

> Only in the maker.transcripts.fasta will have offsets other than 0, you can
> use these to get the transcription offset.  All other *.transcript.fasta files
> will always have an offset of 0 for the reason previously mentioned.  Some
> genes will not start with ATG or have stop codons.  These are partial models.
> Set always_complete=1 to reduce these.


Secondly, there is several files named *.augustus_masked.proteins.fasta,
*.non_overlapping_ab_initio.proteins.fasta, and *.proteins.fasta. What is
the criteria of splitting those files?
> Final selected annotations go in the maker.proteins.fasta and
> maker.transcripts.fasta files.  Raw unfiltered ab initio prediction from
> augustus go in the augustus_masked.proteins.fasta and
> augustus_masked.transcripts.fasta file (these are for reference purposes).  A
> set of non-redundant rejected models go in the
> non-overlapping.transcripts.fasta and  non-overlapping.proteins.fasta files
> (if you are missing a gene you expected to find, look in this file first ­ you
> can add them back if you find protein domains in them for example).


The reason why I¹m asking is that some genes were redundant between
*.augustus_masked.proteins.fasta and *.proteins.fasta.
> This is because some of the augustus generated models made it into the final
> annotation set.
> 
> 
Thanks,
Carson

From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Sunday, April 07, 2013 12:13 AM
To: Michael Thon; Kang, Yang Jae
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] CDS retrieve from augustus_masked
 

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
<mailto: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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