[maker-devel] Question about re-annotation

[Carson Holt]

If you are running several times, just rerun in the same directory after altering settings. MAKER will reuse old raw data reports as appropriate. The maker_gff option is really just for reannotating from an old maker run where you no longer have the raw files available.

—Carson


> On Apr 2, 2020, at 12:24 PM, Thodoris Danis <danis_theo at hotmail.com> wrote:
> 
> Hello maker community,
> 
> 
> I am annotating a fish genome with Maker 2.31.10, for which I have transcript evidence and proteins from closely related species. I am running maker in several passes and pass the gff output to the nest pass every time here (
>> 
>> "#-----Re-annotation Using MAKER Derived GFF3
>> maker_gff= #re-annotate genome based on this gff3 file",
> ), is this wrong? and where is the difference running the maker from scratch without re-supplying every time the new gff?
> 
> Secondly,  in the second round after predictors training, have I to keep est2genome=1 , protein2genome=1, ests and proteins evidence or not?
> How do we switch all thesre parameters? 
> 
> Any input from experienced maker users is welcome
> Thank you for your help
> 
> 
> Θεόδωρος Δανης 
> Thodoris Danis
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