[maker-devel] [CAUTION: Suspicious Link] map_forward=1 not mapping reference ID's to output correctly

[Carson Holt]

A quick overview of MAKER behavior. MAKER will keep everything in model_gff as long as you don’t provide another predictor to run or pred_gff file to use. But if you give it a predictor to run, it takes that as an indicator that you want to update models. So model_gff may get replaced by another prediction that overlaps it but scores better.

So depending on the behavior you want, make sure you are using model_gff and do or don’t provide a gene predictor to run.

—Carson



> On Jun 22, 2018, at 2:04 PM, Poelchau, Monica <monica.poelchau at ars.usda.gov> wrote:
> 
> Hi Kapeel,
>  
> If you just want your community annotations to replace models in an existing gene set, we have a tool for this:
>  
> https://github.com/NAL-i5K/GFF3toolkit <https://github.com/NAL-i5K/GFF3toolkit>
>  
> You’d need to run gff3_QC on your annotation files first to make sure your annotations are okay, then use gff3_merge to merge your community annotations with your existing gene set (in gff3 format). If you end up trying this out - we’re actively developing the GFF3toolkit, so feel free to post an issue if you notice any problems.
>  
> Hth,
>  
> Monica 
>  
> From: maker-devel <maker-devel-bounces at yandell-lab.org <mailto:maker-devel-bounces at yandell-lab.org>> on behalf of Kapeel Chougule <kapeelc at gmail.com <mailto:kapeelc at gmail.com>>
> Date: Friday, June 22, 2018 at 13:53
> To: "maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> Subject: [CAUTION: Suspicious Link][maker-devel] map_forward=1 not mapping reference ID's to output correctly
>  
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> Questions: Spam.Abuse at wdc.usda.gov <mailto:Spam.Abuse at wdc.usda.gov>
> 
> Hi,
>  
> I am trying to update community annotation <https://de.cyverse.org/dl/d/39D60E88-078D-4CF5-9F3A-D712B714CDD8/community.annotation.gff3> in the light of new evidence data but my MAKER runs are not keeping all the genes from the community annotation.
> 
> 
> Community annotation feature count: 2 1 bicolor 239969 CDS 266301 exon 51066 five_prime_UTR 34129 gene 47121 mRNA 53708 three_prime_UTR
> MAKER gene count->  
> awk '$3=="gene"{print}' maker_output.all.gff | grep "Sobic*" | wc -l 21105
>  
> In the maker_opts.ctl file attached, I did make keep_preds=1 and map_forward=1 which keep all the community gene models even if they dont have evidence support. This was explained here:
> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data <http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data>
> . So not sure why we dont have the all the community gene models mapped in the MAKER output
> 
> Thanks
> 
> Kapeel
> -- 
>  
> Kapeel Chougule
> Computational Scientist Developer II
> One Bungtown Road Cold Spring Harbor, NY 11724
> http://www.warelab.org/ <http://www.warelab.org/>
> 
> 
> 
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