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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Ranjani,
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<div>Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. </div>
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<div>Thanks,</div>
<div>Daniel</div>
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<div class="PlainText">Daniel Ence<br>
Graduate Student<br>
Eccles Institute of Human Genetics<br>
University of Utah<br>
15 North 2030 East, Room 2100<br>
Salt Lake City, UT 84112-5330</div>
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<div id="divRpF701003" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> maker-devel-bounces@yandell-lab.org [maker-devel-bounces@yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani@uga.edu]<br>
<b>Sent:</b> Wednesday, January 16, 2013 9:16 AM<br>
<b>To:</b> maker-devel@yandell-lab.org<br>
<b>Subject:</b> [maker-devel] Transcriptome data to gene models<br>
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<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Hi,<br>
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I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and
turned off all gene predictors<br>
But I find gene models are not generated for all transcripts only about half of them.
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Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision?<br>
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Thanks,<br>
Ranjani<br>
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