[maker-devel] Single exon EST and UTR annotation?

[Marc Höppner]

Hi,

we are currently annotating a fungus with essentially no introns. Training of augustus was performed on an ‘evidence’ build and resulting performance of the abinit profile was very good overall. But it seems that maker never makes UTRs for these single exon genes, despite setting:

single_exon=1
single_length=100

I can see in the resulting gff files that the cufflinks transcripts were processed through and visual inspection of the entire data set in WebApollo suggests that we should see UTRs for most genes. Yet there are none. 

(we have used Maker before, so basic usage is familiar, and we have never seen this issue until this project).

Maker version is 2.31-8

Is it verified that the single_exon option works? Are there any other not-so-obvious reasons for the behaviour we see here?

Cheers,

Marc

Marc P. Hoeppner, PhD
Team Leader
Department for Medical Biochemistry and Microbiology
Uppsala University, Sweden
marc.hoeppner at imbim.uu.se