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

[Carson Holt]

Hey Dave,

I sent Bob a pre-release version of MAKER that handles everything much more seamlessly, but I only sent it to him directly because I didn't want the link going to everyone on the maker-devel mailing list.

>>>Here are the contents

Yes, there is a way.  I've detailed it before, but it actually takes more steps than I'd like, so in the new version of MAKER I've built a separate script to do this outside of MAKER.

Here is a link to the new pre-release version of MAKER ->
http://www.yandell-lab.org/research/maker.tar.gz

Once you've installed it, the script is map2assembly in the maker/bin directory.  Just supply the new genome assembly in fasta format and a transcript multi-fasta file for the old gene models.  The output is a new GFF3 file written in the current working directory (it will be named after the input genome assembly file).

Note: One new feature in this pre-release version of MAKER is the ability to start multiple script instances at the same time.  The scripts will then talk to each other (even across systems) and parallelize the workload.  This means if you have spare processors you can start another instance of maker or map2assembly at any time and they will jump in and start working with the other pre-existing instances seamlessly.

Thanks,
Carson


On 12/17/09 4:09 PM, "Dave Clements, GMOD Help Desk" <help at gmod.org> 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
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>
>



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