[Gmod-help] Re: [maker-devel] coordinates re-mapping question

[Bob Freeman]

Dave,

Replying privately as Carson sent me (privately) a link to a beta that  
he's releasing. I haven't yet had the chance to download the software  
and give it a try.

Thanks for being on top of this, though.

-b

On Dec 17, 2009, at 6:09 PM, Dave Clements, GMOD Help Desk wrote:

> Hi Bob,
>
> Catching up on e-mail ...
>
> On Thu, Dec 10, 2009 at 10:03 AM, Bob Freeman
> <bob_freeman at hms.harvard.edu> wrote:
>> Carson et al.,
>> I seem to recall a note from you or a note hitting this list that  
>> MAKER can
>> handle remapping coordinates. How does one go about doing this??
>
> From Carson's earlier email:
> ----------------------
> MAKER will do this.  Currently it is a two step process, in the next
> MAKER release this will be just one step.  Just supply transcripts
> from the old assembly as ESTs to MAKER, then set the predictor to
> est2genome (turn repeatmasking options off by setting them to empty
> values).  This will map everything forward onto the new assembly.
> MAKER at first will destroy the old names because it thinks these are
> ESTs, so it doesn’t give name preservation a priority.  Pulling the
> old names forward is very easy though with just a second step.  Take
> the final MAKER output GFF3 file filter it for the source tag
> est2genome (cat output.gff | grep –P “\test2genome\t” > new.gff).
> Then use this GFF3 file as input for the pred_gff option  in MAKER,
> and set the predictor to pred_gff.  This will map the names forward in
> the final GFF3 file.
> ----------------------
>
> And, um, that's more than I know about MAKER.
>
> Does that help at all?
>
> Dave C.
>
>> Our situation: we obtained gff3 output from AUGUSTUS (independent  
>> of MAKER)
>> for gene models from a 1.0 assembly of our genome. Our current  
>> GBrowse
>> installation is on the 1.0 assembly, and I've loaded this, the gff3  
>> data, as
>> well as nt and protein versions of the models into GBrowse.
>> A v1.1 assembly is now available; although there have been changes  
>> to remove
>> contaminating sequences, I'm not sure how different the assemblies  
>> are. But
>> I need to re-map the 1.0-based gene models onto the 1.1 assembly.
>> How do I proceed with this? Again, I have gff3 output, as well as  
>> nt and
>> protein fasta files that I generated using the gff3 output.
>> Thanks much!
>> Bob
>> -----------------------------------------------------
>> Bob Freeman, Ph.D.
>> Acorn Worm Informatics, Kirschner lab
>> Dept of Systems Biology, Alpert 524
>> Harvard Medical School
>> 200 Longwood Avenue
>> Boston, MA  02115
>> 617/432.2293, vox
>> The only other person I've apologized to is my mother and that was  
>> court
>> ordered.
>> -- Karen Walker from Will & Grace
>>
>>
>>
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>> maker-devel at yandell-lab.org
>> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>
>
>
> -- 
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-----------------------------------------------------
Bob Freeman, Ph.D.
Acorn Worm Informatics, Kirschner lab
Dept of Systems Biology, Alpert 524
Harvard Medical School
200 Longwood Avenue
Boston, MA  02115
617/432.2293, vox

The only other person I've apologized to is my mother and that was  
court ordered.
	-- Karen Walker from Will & Grace