[maker-devel] tRNAscan GFF3

[Carson Holt]

Thanks.

--Carson


From:  Daniel Standage <daniel.standage at gmail.com>
Date:  Tuesday, August 26, 2014 at 9:55 AM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  Maker Mailing List <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] tRNAscan GFF3

Sorry for the delayed response. In the mean time, I wrote a tiny script to
correct the erroneous tRNA annotations. I just now took a few minutes to
download 2.31.6, and can confirm that the tRNA exon strands are consistent.

Best,
Daniel


--
Daniel S. Standage
Ph.D. Candidate
Computational Genome Science Laboratory
Indiana University


On Thu, Aug 21, 2014 at 11:49 AM, Carson Holt <carsonhh at gmail.com> wrote:
> I half way remember some tRNAscan bugs being fixed in several of the sub
> versions of 2.31 (tRNAscan was only introduced as an option in 2.30 I believe
> and most 2.31 updates were related to tRNAscan).  Current version is 2.31.6.
> Could you give it a try and see if it is still giving you the issue.
> 
> I did a quick look through the archives and I think this was found and fixed
> --> 
> https://groups.google.com/forum/#!searchin/maker-devel/trna$20strand/maker-dev
> el/Z-kvf_V2ynU/vstSNjHgyJQJ
> 
> Thanks,
> Carson
> 
> 
> From:  Daniel Standage <daniel.standage at gmail.com>
> Date:  Thursday, August 21, 2014 at 9:36 AM
> To:  Carson Holt <carsonhh at gmail.com>
> Cc:  Maker Mailing List <maker-devel at yandell-lab.org>
> Subject:  Re: [maker-devel] tRNAscan GFF3
> 
> This annotation was generated using Maker 2.31.3.
> 
> 
> --
> Daniel S. Standage
> Ph.D. Candidate
> Computational Genome Science Laboratory
> Indiana University
> 
> 
> On Thu, Aug 21, 2014 at 11:35 AM, Carson Holt <carsonhh at gmail.com> wrote:
>> It should be on the same strand.  Which MAKER version are you using?
>> 
>> --Carson
>> 
>> 
>> From:  Daniel Standage <daniel.standage at gmail.com>
>> Date:  Thursday, August 21, 2014 at 9:33 AM
>> To:  Maker Mailing List <maker-devel at yandell-lab.org>
>> Subject:  [maker-devel] tRNAscan GFF3
>> 
>> Greetings!
>> 
>> I have a quick question about Maker's handling of tRNAscan output,
>> particularly tRNAs containing introns. If I haven't missed something, it
>> looks like Maker reports the second exon on the opposite strand as the first
>> exon, the tRNA feature, and the gene feature? Am I reading this correctly?
>> 
>> I don't think this representation makes sense. The second exon is
>> complementary to the first (hence the folding), but it is not encoded on or
>> transcribed from the opposite strand. Unless I've misunderstood something, I
>> would suggest that the correct representation would be to have all features
>> on the same strand.
>> 
>> Thanks,
>> Daniel
>> 
>> --
>> Daniel S. Standage
>> Ph.D. Candidate
>> Computational Genome Science Laboratory
>> Indiana University
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/ma
>> ker-devel_yandell-lab.org
> 



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