Reviewing Maker annotation

Question

[alslonik]

Hi all. I am working on an annotation a denovo plant genome with Maker pipeline. I am currently at a step of post-processing and there are some things that I am not sure about: I had 3 Maker iterations - an initial one and two consectutive with gene prediction using snap and augustus. I ran a reciprocal blast on this output. It contains some (in my case around ~10%) identical records. I am going to collapse the identical models into one consensus. Are there any additional filters post-annotation do you apply on the output of Maker?

Answer 1

[alslonik]

OK, I'll answer to myself, in case someone will need this in the future. Here is a nice pipeline of post-annotation.