[maker-devel] MAKER: single exons not predicted

[Nicola Palmieri]

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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