[maker-devel] Find evidence for specific gene annotation (without any genome browser!)

[Carson Holt]

It’s based on overlap. If you want to know the specific evidence you take everything that overlap the gene coordinates and cluster that together. Bedtools might be the easiest way to get everything for a given set of coordinates.

For naming based off of protein2genome alignment, one option is to set est_forward=1 in the control files during the maker run (must manually add it). It is a hack for fast protein mapping of previous annotations onto new assemblies.  But you can use it to force naming of any protein source. There are several more examples of using this option in the maker-devel archives —> https://groups.google.com/g/maker-devel/search?q=est_forward

—Carson


> On Jan 22, 2021, at 5:42 AM, Ricardo Nuno Ferreira Martins Guerreiro <guerrer at uni-duesseldorf.de> wrote:
> 
> 
> Hello,
> 
> Simple question:  How do I know which evidence generated one specific gene? Or even, which evidences are used for it's AED calculation?
> 
> How do I do this if the gene is predicted directly by a prot2genome alignment? And how when it's an Augustus annotation?
> 
> I want to do this without Jbrowser, which is a huge waste of time. I want the original name in my input protein set, not the maker name.
> 
> 
> Cheers,
> Ricardo
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 1376 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20210310/e0aa8621/attachment-0002.p7s>