Hi everyone !
I'm trying to do an assembly of a D. suzukii genome, a close related species of D. melanogaster, but with a slighyt bigger genome ( D. mel : 150 M, D. suzukii : about 220M). After the assembly, I want to use maker. But it's my first time using it.
I spend a lot of time reading the manual, which is really detailed : http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial#Genome_Options_.28Required.29
I read that Maker is running some ab inito prediction (like augustus), and then also use some external evidences (EST evidence from the species or a related species, and the same for protein evidence). After that, it try to make a kind of consensus to annotate the genome (if I'm right).
About the input for EST evidence and protein evidence, I was wondering, the manual say that you could give a Fasta file, or (and ? ) a gff file. But I don't know if both are necessary (I don't think so actually, because the little example for the tutorial only used a fasta file). Do we need to add a gff or just a fasta is good ? (Or maybe just a gff is good even if no fasta ?)
Also, as D. suzukii is not really a emerging model organism, as it's closely related to D. melanogaster, do I need to do the train step of ab initio gene predictors ?
Thanks for your answers !