Creating a new gene model

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Creating a new gene model

Robin A. Ohm
Hello,

What is the best way to create a gene model at a locus where the gene
predictors have failed to predict one? For example, fairly often an
RNAseq coverage curve clearly indicates that a gene is present, but no
gene was predicted there. In such a case, there is nothing to drag into
the User Created Annotation track.

Thanks for your help. Best regards,

Robin

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Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016





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Re: Creating a new gene model

Monica Munoz-Torres
Dear Robin, 

Because gene models should only be annotated when there is supporting biological evidence for their existence, the answer to your question is that there is not a "best way" to create a gene model when no evidence supports one. 

In the example you share, RNAseq coverage does show evidence of transcription. Are there RNAseq reads you can use as a starting point for the gene you wish to annotate? (To drag and drop into User-created Annotations area).

Else, one known workaround is to create a GFF3 file that contains the coordinates for the gene model you are trying to annotate. Again, this is only recommended when there is experimental evidence supporting a gene model in these coordinates - and the automated prediction software have failed to call the gene in the region (which seems to be your case). 

Open the GFF3 file using the 'Select files' option in the 'Open Files' box. 
For this, use the 'File' top-level menu in Apollo, and go to 'Open'. A box will pop-up. In the upper left corner there is a space labeled 'Local Files' and inside a button labeled 'Select files' to help you choose the GFF3 file you have created. 

--> File / Open / Local files / Select files / yourfile.gff

This will open a new track of evidence, which you can use to can drag the gene model you need. 

I hope this helps, but please do not hesitate to contact us with further questions.

cheers, 
~moni. 




On Thu, Apr 21, 2016 at 2:01 AM, Robin A. Ohm <[hidden email]> wrote:
Hello,

What is the best way to create a gene model at a locus where the gene predictors have failed to predict one? For example, fairly often an RNAseq coverage curve clearly indicates that a gene is present, but no gene was predicted there. In such a case, there is nothing to drag into the User Created Annotation track.

Thanks for your help. Best regards,

Robin

--
Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | <a href="tel:%2B31%20%280%29%2030%202533016" value="+31302533016" target="_blank">+31 (0) 30 2533016





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Mentorship Matters!
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Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
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Berkeley, CA 94720




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