[maker-devel] custom "ab initio" predictions with automatic hint-based predictions

[Bob Zimmermann]

Hello,

I would like to run maker with a custom set of ab initio predictions (based on hints given to augustus from RNAseq data), but allowing it to incorporate EST and protein data to make an additional run of augustus using hints derived from those alignments. 

My gene prediction section of the maker_opts.ctl file looks like this:
...
augustus_species=all_combined #Augustus gene prediction species model
...
pred_gff=../ab_initio_predictions/all_combined.augustus_masked.gff3 #ab-initio predictions from an external GFF3 file
model_gff= #annotated gene models from an external GFF3 file (annotation pass-through)
est2genome=1 #infer gene predictions directly from ESTs, 1 = yes, 0 = no
protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no
…

It seems as though even if pred_gff is set, augustus will still be run for ab initio predictions with no hints if an augustus_species setting is present. I was curious if there was any way around this, partly because custom ab initios could improve my annotation and also because the ab initio step can take long.

Thanks for your help!

Bob