Using BUSCO to predict gene functions with existing gff/gtf table?
Entering edit mode
2.3 years ago
zhousun21 ▴ 40

Hi all,

I'm trying to predict gene functions for eukaryote genomes. I can get the gene models using GeneMark or Augustus. I'm having trouble assigning gene functions.

Running Busco using Augustus as a component has not been successful (somehow setting the environment variables for Augustus via Busco isn't working correctly, after a lot of attempts by IT guys.) Has anyone been able to use Busco with existing gene models in gtf or gff format?

Extracting protein sequence and running Blast searches on our own dbs works fine but is clunky. It seems there must be a better way.

Can anyone suggest a process that can input a raw assembled eukaryotic fasta and output gene functions?

Any advice will be appreciated.

busco augustus genemark genome annotation • 867 views

Login before adding your answer.

Traffic: 1184 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6