[maker-devel] maker gene prediction and overlapping genes

[Anjuli Meiser]

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