[maker-devel] associating gene names between related strains

[Janna Fierst]

I will try it today. Thanks for the quick reply!


On Fri, Mar 14, 2014 at 10:32 AM, Daniel Ence <dence at genetics.utah.edu>wrote:

>  Hi Janna, So do you have one strain that you want to use as the
> reference for all the others? There's a script that comes with MAKER called
> maker_map_ids that lets you use a common prefix or suffix for entries in a
> fasta file from one strain and then use est_forward to use that ID in the
> gene models for the other species.
>
>  Let me know if that's not what you're looking for,
> Daniel
>
>  Daniel Ence
> Graduate Student
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
>   ------------------------------
> *From:* maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of
> Janna Fierst [jfierst at uoregon.edu]
> *Sent:* Friday, March 14, 2014 10:06 AM
> *To:* maker-devel at yandell-lab.org
> *Subject:* [maker-devel] associating gene names between related strains
>
>   Hi,
>
> we are assembling and annotating genomes for several related strains of
> Caenorhabditis worms and I was wondering if there is a way to coordinate
> the gene naming so that orthologs between species can be associated by
> name. I have been playing around a little with the est_forward option but
> can't figure out a good system/workflow that preserves names but still uses
> the strain-specific RNA-Seq EST set for the actual gene models. Thanks!
> -Janna
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20140314/6c26531d/attachment-0003.html>