[maker-devel] tRNAscan GFF3

[Carson Holt]

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-d
evel/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
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