Augustus Gene Frequency and Gene Names (Using BRAKER Pipeline)

Question

[isu2017]

Hi everyone,

I recently finished running the braker pipeline on a previously unannotated organism. The pipeline just finished, with the final GTF file from Augustus being produced. However, the total amount of genes in his the file are much larger than what we expected (close to 100,000 were predicted.) Additionally, each gene is labeled as "gene1", "gene2", ect. So, my questions are:

1.) How can I reduce the redundancy in the amount of predicted genes. 2.) How can I annotate the genes and retrieve gene names

Thanks!

Answer 1

[isu2017]

Any ideas would be greatly appreciative!