Good to know. Thanks for your help!<br clear="all"><br>--<br>Daniel S. Standage<br>Ph.D. Candidate<br>Bioinformatics and Computational Biology Program<br>Department of Genetics, Development, and Cell Biology<br>Iowa State University<br>
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<br><br><div class="gmail_quote">On Thu, Oct 4, 2012 at 3:19 PM, Carson Holt <span dir="ltr"><<a href="mailto:Carson.Holt@oicr.on.ca" target="_blank">Carson.Holt@oicr.on.ca</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div>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.</div>
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<div>Thanks,</div>
<div>Carson</div>
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<span style="font-weight:bold">From: </span>Daniel Standage <<a href="mailto:daniel.standage@gmail.com" target="_blank">daniel.standage@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, 4 October, 2012 3:16 PM<div><div class="h5"><br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br>
<span style="font-weight:bold">Cc: </span>Maker Mailing List <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] Expected format for EST GFF3<br>
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Does the cufflinks2gff3 script filter out single-exon transcripts?<br clear="all">
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--<br>
Daniel S. Standage<br>
Ph.D. Candidate<br>
Bioinformatics and Computational Biology Program<br>
Department of Genetics, Development, and Cell Biology<br>
Iowa State University<br>
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<div class="gmail_quote">On Thu, Oct 4, 2012 at 3:09 PM, Carson Holt <span dir="ltr">
<<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br>
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<div>Use the cufflinks2gff3 script that comes with MAKER.</div>
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<div>Thanks,</div>
<div>Carson</div>
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<span style="font-weight:bold">From: </span>Daniel Standage <<a href="mailto:daniel.standage@gmail.com" target="_blank">daniel.standage@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, 4 October, 2012 3:07 PM<br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br>
<span style="font-weight:bold">Cc: </span>Maker Mailing List <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] Expected format for EST GFF3<br>
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Great. I am using PE Illumina reads mapped by Tophat and assembled by Cufflinks. The GTF file Cufflinks produces only
<b>transcript</b> and <b>exon</b> features. So I'm assuming I can simply convert the
<b>transcript</b> features to <b>match</b> and the <b>exon</b> features to <b>match_part
</b>and make sure the parent/child relationships are maintained with the <b>Parent</b> and
<b>ID</b> attributes?<br clear="all">
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--<br>
Daniel S. Standage<br>
Ph.D. Candidate<br>
Bioinformatics and Computational Biology Program<br>
Department of Genetics, Development, and Cell Biology<br>
Iowa State University<br>
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<div class="gmail_quote">On Thu, Oct 4, 2012 at 2:58 PM, Carson Holt <span dir="ltr">
<<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br>
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<div>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.</div>
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<div>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.</div>
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<div>Thanks,</div>
<div>Carson</div>
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<span style="font-weight:bold">From: </span>Daniel Standage <<a href="mailto:daniel.standage@gmail.com" target="_blank">daniel.standage@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, 4 October, 2012 2:52 PM<br>
<span style="font-weight:bold">To: </span>Maker Mailing List <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>[maker-devel] Expected format for EST GFF3<br>
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Greetings.
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<div>I would like to use Maker's <b>est_gff</b> 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!<br clear="all">
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--<br>
Daniel S. Standage<br>
Ph.D. Candidate<br>
Bioinformatics and Computational Biology Program<br>
Department of Genetics, Development, and Cell Biology<br>
Iowa State University<br>
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