[maker-devel] gene annotation for a better genome

[Carson Holt]

You can try using the est2genome=1 option to map the old models forward onto the new assembly as if they were ESTs (add a line that says est_forward=1 to the control file to maintain old naming and set est=1 to the old model transcript file). Then provide the final models as a pred_gff for a subsuquent run (i.e. a traditional MAKER run where you are annotating the new assembly with transcript and protein evidence and ab initio predictors). Don’t supply the old models to est= on that run.

The idea behind doing it this way is:
1. You need to get old models onto the new assembly so coordinates will change. So by doing it this way, you will at least be able to move many models forward based on homology.
2. By providing the models to pred_gff on a subsequent MAKER run, you are just letting old models compete against new annotations. They will be rejected if they have no evidence support, or can be kept if they score better than alternate models from SNAP/Augustus. That way you have the chance to integrate old models while at the same time rejecting some old models that have no evidence overlap.

—Carson


> On Sep 28, 2017, at 6:05 AM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> Hello:
> 
> Recently, we got a new version of NMR genome, whose genome had been assembled and annotated a few years ago. We can download the gene annotation from NCBI. 
> 
> Now we want to annotate the new genome using Maker2 pipeline. I wonder how can I fully make use of existing annotations. On the other hand, since the previous genome is not very well assemblies, some genes annotation maybe false positives. I hope those false positive genes in previous annotation won't mislead Maker2 for current gene annotation.
> 
> Do you have any suggestions. Thanks
> 
> Best
> Quanwei  
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