Hi everyone !
I'm aiming to fully assemble and annotate the D. suzukii genome. For the annotation part, it is my first time, I already asked a lot of questions here, and get a lot of answers, but some points remains very unclear to me, even in the Maker tutorial (http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial#Merge.2FResolve_Legacy_Annotations ).
In their tutorial, they fully described the procedure to train SNAP. So we have to launch several times maker in order to produce a final pyu.hmm, corresponding to the "final" SNAP model that I'm going to give to my "final" maker.
I was looking for something similar for Augustus, but couldn't really find what I wanted.
So what I did, is to run myself Augustus, first abinitio, and then giving hints (some RNAseq data that correspond to my organism).
I was aiming to give theses 2 augustus output file to maker using for example the maker_opts.ctl :
... est_gff= #aligned ESTs or mRNA-seq from an external GFF3 file ... pred_gff= #ab-initio predictions from an external GFF3 file model_gff= #annotated gene models from an external GFF3 file (annotation pass-through) ... other_gff= #extra features to pass-through to final MAKER generated GFF3 file
But as you see, there is a lot of places where I could provide my augustus GFF, and I'm not really confident about how theses parameters are similar, or how they affect the final annotation... Also not sure that I'm doing the right thing, and that I'm really "training" augustus or not.
Can I have some advices please ?