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

[Carson Holt]

Actually , the issue is that single exon genes have a higher threshold to meet to get UTR.  Also MAKER will never add spliced UTR to a single exon gene, so an EST would also have to be single exon and encompass the entire single exon gene to get UTR.  This is done because EST and mRNA-seq data in general is noisy enough that you will get mostly false UTR annotations otherwise. So it is an overly conservative approach because it’s the best of all the bad options.  For spliced genes, the splice site can be used to confirm concordance of the UTR with the gene, but that can’t be done with single exon calls.

—Carson

> On Feb 20, 2015, at 11:01 AM, Daniel Ence <dence at genetics.utah.edu> wrote:
> 
> Hi Marc, 
> 
> Does Maker annotate the single-exon genes and miss the UTRs or is it missing the single-exon genes entirely? 
> 
> There’s another option in the control file called “correct_est_fusion”. This option was added because of difficulties we encountered in a fungal genome annotation project where the genome had lots of overlapping UTRs in genes. The overlapping UTRs resulted in lots of fused genes, so the solution was to add this option to limit the use of ESTs in annotation genes. Basically, if “correct_est_fusion” is turned on, Maker won’t annotate UTRs that would result in fused gene models. 
> 
> Are these single-exon genes really close together? That and the setting that I discussed above could explain the lack of UTRs. 
> 
> ~Daniel
> 
> 
> 
> 
> 
>> On Feb 20, 2015, at 7:53 AM, Marc Höppner <marc.hoeppner at imbim.uu.se> wrote:
>> 
>> 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
>> 
>> 
>> 
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