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

[Ricardo Nuno Ferreira Martins Guerreiro]

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...@yandell-lab.org
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

[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