[maker-devel] maker gene prediction and overlapping genes

[Michael Thon]

In my case I did find two overlapping gene preditions on opposite strands from different ab initio gene predictors where neither model has est or protein support.  Most of the cases though are where one model has support but not the other so we will probably fix them manually.

Thanks for your help

 
> On Sep 28, 2015, at 5:51 PM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> 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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