[maker-devel] associating gene names between related strains

[Daniel Ence]

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
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