[maker-devel] gff output

[Muriel Gros-Balthazard]

Hello,

I have been using Maker to generate an annotation.
I especially set these options:
- est_gff with a list of transcripts.gff3 (Cufflinks output)
- model_org=all
- rmlib=allrepeats.lib
- repeat_protein=te_prot.fasta
- pred_gff= Augustus.gff3 (that I generated previously)

I obtain a gff file for each of my contigs.
However, here are the three possibilities in the second column :
# est_gff:cufflinks
# repeatmasker
# repeatrunner

I have no information about exons and introns.
And I am wondering if the Augustus.gff3 was used...

On top of that, I forgot to set up pred_stats to 1.
If I understand well, I can just change this in the ocntrol file, and 
run Maker again. Since there is the output with everything, it won't run 
again the prediction, only this option. Is that right ?

Thank you,

Muriel