[maker-devel] maker gene prediction and overlapping genes

[Carson Holt]

Basically you have evidence spuriously aligning to both strands.  This means either your repeat masking is insufficient or your EST/mRNA-seq evidence is noisy and generating a lot of false alignments.  You may need to turn off single_exon if you rare using it, or reassemble any short read evidence to try and improve the specificity of the alignments.  I believe some of the previous responses to your post suggested methods to do this with trinity.

—Carson


> 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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