[maker-devel] Expected format for EST GFF3

[Daniel Standage]

Does the cufflinks2gff3 script filter out single-exon transcripts?

--
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 3:09 PM, Carson Holt <carsonhh at gmail.com> wrote:

> 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
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>>
>
>
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