[maker-devel] Expected format for EST GFF3

[Carson Holt]

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<mailto:daniel.standage at gmail.com>>
Date: Thursday, 4 October, 2012 3:16 PM
To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Cc: Maker Mailing List <maker-devel at yandell-lab.org<mailto: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<mailto:carsonhh at gmail.com>> wrote:
Use the cufflinks2gff3 script that comes with MAKER.

Thanks,
Carson


From: Daniel Standage <daniel.standage at gmail.com<mailto:daniel.standage at gmail.com>>
Date: Thursday, 4 October, 2012 3:07 PM
To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Cc: Maker Mailing List <maker-devel at yandell-lab.org<mailto: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<mailto: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<mailto:daniel.standage at gmail.com>>
Date: Thursday, 4 October, 2012 2:52 PM
To: Maker Mailing List <maker-devel at yandell-lab.org<mailto: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<mailto:maker-devel at box290.bluehost.com>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20121004/82dcb7f3/attachment-0002.html>