[maker-devel] MAKER: single exons not predicted

[Carson Holt]

Most single exon alignments from ESTs or mRNA-seq will actually be spurious in nature. It’s the reason why single exon alignments are ignored by default. Also as Daniel mentioned, gene predictors do not like to call single exon genes. Maker gets around this by supplying hints to the predictor based on alignment evidence which increases the probabilities of the HMM used by the predictor within a given region, but given the spurious nature of single exon nucleotide alignments, you will also need protein alignment support for single exon genes for this to work.

Also the region you gave as an example does not appear to be an open reading frame. In fact almost the entire region that overlaps the Augustus call is labeled as UTR. It looks like a classic spurious alignment.  Likely an unmasked repetitive element.

—Carson




> On Aug 4, 2015, at 10:03 AM, Daniel Ence <dence at genetics.utah.edu> wrote:
> 
> 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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