[maker-devel] Expected format for EST GFF3

[Carson Holt]

Use the cufflinks2gff3 script that comes with MAKER.

Thanks,
Carson


From:  Daniel Standage <daniel.standage at gmail.com>
Date:  Thursday, 4 October, 2012 3:07 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  Maker Mailing List <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Expected format for EST GFF3

Great. I am using PE Illumina reads mapped by Tophat and assembled by
Cufflinks. The GTF file Cufflinks produces only transcript and exon
features. So I'm assuming I can simply convert the transcript features to
match and the exon features to match_part and make sure the parent/child
relationships are maintained with the Parent and ID attributes?

--
Daniel S. Standage
Ph.D. Candidate
Bioinformatics and Computational Biology Program
Department of Genetics, Development, and Cell Biology
Iowa State University



On Thu, Oct 4, 2012 at 2:58 PM, Carson Holt <carsonhh at gmail.com> wrote:
> Match/match_part features are expected.  MAKER expects these to be polished
> (I.e. correctly aligned around splice sites).  For example exonerate, BLAT,
> and cufflinks results will be correct around splice sites and can be used;
> BLAST results on the other hand will not be correct and should not be used.
> 
> The Gap attribute is used by maker if available, but is not required (Gap
> describes how to reconstruct an alignment for gaps and mismatches).  Otherwise
> MAKER assumes all positions are matches to the reference.
> 
> Thanks,
> Carson
> 
> 
> From:  Daniel Standage <daniel.standage at gmail.com>
> Date:  Thursday, 4 October, 2012 2:52 PM
> To:  Maker Mailing List <maker-devel at yandell-lab.org>
> Subject:  [maker-devel] Expected format for EST GFF3
> 
> Greetings.
> 
> I would like to use Maker's est_gff option to include EST evidence from an
> external GFF3 file. In addition to being a valid, well-formed GFF3 file, what
> expectations does Maker assume about the contents of this file? Which feature
> types are expected and/or supported? Thanks!
> 
> --
> Daniel S. Standage
> Ph.D. Candidate
> Bioinformatics and Computational Biology Program
> Department of Genetics, Development, and Cell Biology
> Iowa State University
> 
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/mak
> er-devel_yandell-lab.org



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