Downloading gff of curated gene set

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Downloading gff of curated gene set

Alisa Postma
I am struggling to download the gff for a specific version of our genome annotation after curation. When I download the gff from the user annotation space, it only gives me a gff containing the gene models and "work in progress" which are present in that space. And when I download from the maker track, I get the static, original gene models without the latest curations which had been done. 
I would like to "freeze" the annotation curation in it's current state and download all the original gene models for those genes which have not been edited as well as the curated models for those which have been. 
Any help with this would be greatly appreciated.

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Re: Downloading gff of curated gene set

nathandunn

So, if I understand what you want is a way to download a track merged between the user annotation and the evidence track.

This is something we have thought about and would like to do both automatically and properly by designating an official gene set (in your case the maker track): https://github.com/GMOD/Apollo/issues/138

A lot of the complexity comes with updating isoforms. 

However, in the interim what most people do is merge these by hand using Perl or Python scripts.   

If there is some simple short term logic that might be beneficial to you, we’d be happy to take a look at integrating it. 

Thanks,

Nathan


On Jul 12, 2019, at 2:44 AM, Alisa Postma <[hidden email]> wrote:

I am struggling to download the gff for a specific version of our genome annotation after curation. When I download the gff from the user annotation space, it only gives me a gff containing the gene models and "work in progress" which are present in that space. And when I download from the maker track, I get the static, original gene models without the latest curations which had been done. 
I would like to "freeze" the annotation curation in it's current state and download all the original gene models for those genes which have not been edited as well as the curated models for those which have been. 
Any help with this would be greatly appreciated.

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To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].