[maker-devel] Possible ways to improve annotated gene numbers

[Qihua Liang]

Dear Maker Development Team,

Hi, I am using Maker for annotation and BUSCO to evaluate the completeness. 

For de novo perditions, I am using Augustus, GeneMark, and SNAP, and the annotated proteins have completeness of ~80%, ~50%, ~50% correspondingly. When I cat all de novo annotated proteins of these three tools, the completeness is much higher as ~92%. 

But for all.maker.proteins.fasta, the completeness is only ~80%.

1. Does this mean that some proteins annotated by Augustus/GeneMark/SNAP, are not included in the file all.maker.proteins.fasta? Does it because such excluded proteins do not have hits with the EST evidences?

2. To achieve a higher BUSCO completeness, what possible ways can be used? Including more EST evidences from other species?


Thank you
Qihua