[maker-devel] Expected format for EST GFF3

[Daniel Standage]

Good to know. Thanks for your help!

--
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 3:19 PM, Carson Holt <Carson.Holt at oicr.on.ca> wrote:

>   Yes.  You really have to because the single exon transcripts produced
> from mRNA-seq assembly are strandless (you don't know where they belong).
>  They also tend to be heavily weighted to pseudogenes and transposons.
>
>  Thanks,
> Carson
>
>
>
>
>   From: Daniel Standage <daniel.standage at gmail.com>
> Date: Thursday, 4 October, 2012 3:16 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
>
>  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 maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>
>>
>
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