[maker-devel] MAKER: single exons not predicted

[Daniel Ence]

Hi Nicola, I don’t think that August will predict single-exon genes in most cases. That’s probably responsible for your results.

~Daniel

Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

On Aug 4, 2015, at 8:46 AM, Nicola Palmieri <palmierinico at gmail.com<mailto:palmierinico at gmail.com>> wrote:

Dear MAKER developers,

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.

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.

I would really appreciate some hints on how to proceed.

Kind regards,
Nicola

--
Nicola Palmieri
Postdoctoral fellow
Institut für Parasitologie
Vetmeduni Vienna
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