[maker-devel] Missing UTRs in GFF

Tue Apr 1 12:36:44 MDT 2014

It was indeed caused by the correct_est_fusion=1 option (which is supposed
to trim off UTR if it appears overlap of UTR across genes is caused by
merged mRNAseq).  I have attached a patch that is used to replace
.../maker/lib/maker/auto_annotator.pm, and I've updated the website download
to include the patch as in MAKER download version 2.31.3.

Thanks,
Carson

From:  Benjamin Rubin <brubin at fieldmuseum.org>
Date:  Tuesday, April 1, 2014 at 9:21 AM
To:  Carson Holt <carsonhh at gmail.com>
Subject:  Re: [maker-devel] Missing UTRs in GFF

OK, I think I uploaded everything. I included a cleaned up version of the
control file without all of my paths in case that is useful.

Thanks,
Ben

On Tue, Apr 1, 2014 at 9:50 AM, Carson Holt <carsonhh at gmail.com> wrote:
> Could upload your input fasta and hmm files as well.  Sometimes I can
> reproduce errors using just the raw reports, but it looks like I will need the
> input files.
> 
> --Carson
> 
> 
> From:  Benjamin Rubin <brubin at fieldmuseum.org>
> Date:  Tuesday, April 1, 2014 at 8:38 AM
> To:  Carson Holt <carsonhh at gmail.com>
> Subject:  Re: [maker-devel] Missing UTRs in GFF
> 
> Hi Carson,
> 
> I tried using version 2.31 on a scaffold where this problem occurred with 2.30
> and got the same result, unfortunately. I did use corr_est_fusion=1 both times
> so this might be related. I have uploaded the sequence for this scaffold and
> the output directory under username "brubin". Is this the data that you meant?
> 
> I am also reattaching information on a representative problem gene from this
> scaffold that occurs at base 1330779.
> 
> Thanks so much for the help,
> Ben
> 
> 
> On Mon, Mar 31, 2014 at 9:37 AM, Carson Holt <carsonhh at gmail.com> wrote:
>> 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 <tel:%28312%29%20665-7776>
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/ma
>> ker-devel_yandell-lab.org
> 
> 
> 
> -- 
> _____________________________________________________
> 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 <tel:%28312%29%20665-7776>

-- 
_____________________________________________________
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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