I am a phD student working on de novo assembly and annotation of a bird genome. I used Maker as annotation pipeline, which ran very well, and I obtained different annotations with evidence from Augustus gene predictor, small EST dataset from my organism and protein sequences from chicken, turkey and zebrafinch. I could combine the different gff files from different scaffolds into one gff file with annotations for the entire genome.
I now have two questions:
What could be the reason that I haven't gotten the protein.fasta and trancript.fasta files
How can I obtain a consensus gene list of different evidences from maker? What I would actually need is the scaffold, coordinates and annotation (gene name) according to the 3 other bird species. Thank you in advance.
Diana Le Duc