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Hi Nicola, I don’t think that August will predict single-exon genes in most cases. That’s probably responsible for your results.
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<div class="">~Daniel</div>
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<div class="">Daniel Ence</div>
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<div apple-content-edited="true" class="">Graduate Student<br class="">
Eccles Institute of Human Genetics<br class="">
University of Utah<br class="">
15 North 2030 East, Room 2100<br class="">
Salt Lake City, UT 84112-5330 </div>
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<div class="">On Aug 4, 2015, at 8:46 AM, Nicola Palmieri <<a href="mailto:palmierinico@gmail.com" class="">palmierinico@gmail.com</a>> wrote:</div>
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<div dir="ltr" class=""><span style="font-size:12.8000001907349px" class="">Dear MAKER developers,</span>
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<div style="font-size:12.8000001907349px" class="">I am using Maker to annotate a new protozoan species (Cystoisospora suis), I am trying to incorporate TopHat/Cufflinks evidence from RNA-Seq but some genes still do not get annotated.</div>
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<div style="font-size:12.8000001907349px" class="">I attached a screenshot from IGV, in which I use separately Augustus, Cufflinks and then various run of Maker incorporating TopHat and /or Cufflinks as evidence. The single exon genes are constantly not predicted
(ie. gene under the label g.38.t1). I have also played around with the single_exon option. I didn't find any similar post in the wiki.</div>
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<div style="font-size:12.8000001907349px" class="">I would really appreciate some hints on how to proceed.</div>
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<div style="font-size:12.8000001907349px" class="">Kind regards,<br class="">
Nicola</div>
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-- <br class="">
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<div dir="ltr" class="">Nicola Palmieri
<div class="">Postdoctoral fellow<br class="">
Institut für Parasitologie
<div class="">Vetmeduni Vienna</div>
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<span id="cid:8889F48F-DA7C-4588-917B-0D00CD2C5D53@genetics.utah.edu"><Screen Shot 2015-08-04 at 16.39.26.png></span>_______________________________________________<br class="">
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