[maker-devel] maker gene prediction and overlapping genes

[Janna Fierst]

We had this problem with a nematode genome, also with very dense genes. We
partially addressed it by assembling the RNA-Seq with Trinity and clipping
the 5'/3' UTRs, then running with correst_est_fusion.

On Thu, Sep 24, 2015 at 11:23 PM, Michael Thon <mike.thon at gmail.com> wrote:

> Hi all -
>
> We've been having the same problem. In every case I've examined manually
> the overlapping gene models have overlapping CDSs and they are on opposite
> strands. In most cases its easy to see which is the correct model because
> one has protein or EST/RNA-Seq evidence and the other does not. Most times
> one model is from Augustus and the other is from genemark, but not always.
> I found one in which both gene models were from augustus and maker promoted
> both of them.
>
> I count 121 overlaps in our annotation (its a fungal genome). We're about
> to just go in and remove them manually but I want to see if there is any
> way to fix my configuration of maker first.
>
> Mike
>
>
>
> > On Sep 24, 2015, at 8:02 PM, Daniel Ence <dence at genetics.utah.edu>
> wrote:
> >
> > Hi Anjuli,
> >
> > The approach that you outlined sounds pretty reasonable, and I’m not
> certain I understand the problem with your results. Are the short genes
> that lie completely in other genes in the introns? Or do you mean that you
> have overlapping predictions?
> >
> > A common observation in compact fungal genomes is that maker can produce
> gene models that fuse several adjacent genes together. Could that be what
> you’re observing? There's actually an option in maker to deal with that
> issue; it’s the “correct_est_fusion” setting in the opts control file.
> >
> > Let me know whether that helps,
> > 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 Sep 23, 2015, at 2:08 AM, Anjuli Meiser <anjuli.meiser at gmail.com>
> wrote:
> >>
> >> Hello,
> >>
> >> I am using Maker in two rounds for gene prediction in fungal genomes.
> >>
> >> In the first round I'm running maker with the HMMs gained from GeneMark
> and snap with hints from CEGMA and include RNA evidence through a tophat
> gff. Then I convert the maker results to new snap HMMs and augustus HMMs
> and run maker in a second round. I also rescue rejected gene models (maker
> standard build) by running interproscan.
> >>
> >> I observed that I get around 10-15% of genes that are overlapping in
> some way. That includes short genes predicted to lie completely within the
> boundaries of larger genes and also normally overlapping (mostly on
> opposite strands).
> >>
> >> Do you have a suggesting how to deal with this? Did I miss some
> settings in maker to reduce these or at least filter out the shorter genes
> that are lying within other genes?
> >>
> >> Thank you very much in advance for any help in this matter!
> >>
> >> Best wishes,
> >> Anjuli
> >>
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>
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-- 
Janna L. Fierst
Assistant Professor
Department of Biological Sciences
The University of Alabama
Tuscaloosa, AL 35847
Office:  SEC 1339
Phone: 205-248-1830
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