custom "ab initio" predictions with automatic hint-based predictions

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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
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Re: custom "ab initio" predictions with automatic hint-based predictions

Carson Holt-2
Hi Bob,

pred_gff is a way to get models MAKER cannot run into the analysis. Input to pred_gff will not get hints since MAKER is not running the program. Setting augustus_species allows MAKER to run Augustus with and without hints and then those models compete against each other. You cannot just run with hints as the raw model is also used as a filter to help reduce false positive gene models that result from bad hints. If the gff3 you are providing is the same as the MAKER run of Augustus, I would recommend not providing it. If it is different in some way, then you can leave it in.  If you run under MPI (it’s ok to run MPI on a single machine), then MAKER will parallelize the Augustus run by running multiple configs and contig chunks at the same time.

Thanks,
Carson





> On Oct 11, 2017, at 1:42 PM, Bob Zimmermann <[hidden email]> wrote:
>
> 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
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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