[maker-devel] Missing UTRs in GFF

[Carson Holt]

Not something I've seen before, but there was a patch for another issue that
was cause by the use of avoid_est_fusion=1, that may be related.  Try the
current stable release 2.31, and let me know if it still happens.

You can also upload the contig folder from one of the regions in question
here --> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi

Then I could verify the bug, and see if it is something that happens in the
current release.

--Carson


From:  Benjamin Rubin <brubin at fieldmuseum.org>
Date:  Saturday, March 29, 2014 at 10:24 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Missing UTRs in GFF

I have annotated a eukaryotic genome with MAKER 2.30. I recently realized
that there are a few genes in the GFF file produced by gff3_merge with
inconsistencies in the annotated CDS and UTRs. For most of my genes, the
UTRs have their own lines in the GFF file. However, for the problematic
genes, the UTRs are not specified in the GFF file and all exons are
annotated as CDS. The UTRs do appear in the gene header and the protein
sequences are the correct length (do not include the UTR). I have attached
an example from the GFF file.

Is this a known problem, or have I done something wrong? Is there an easy
way to fix the GFF file?

Thanks for your help,
Ben

-- 
_____________________________________________________
Benjamin ER Rubin
PhD Candidate
Committee on Evolutionary Biology
University of Chicago
benrubin.org <http://benrubin.org>

Division of Insects
Zoology Department
Field Museum of Natural History
1400 South Lake Shore Drive
Chicago, IL 60605
USA
Office: (312) 665-7776
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