[maker-devel] Expected format for EST GFF3

[Daniel Standage]

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
>
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>
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