Question about re-annotation

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Question about re-annotation

Thodoris Danis
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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Re: Question about re-annotation

Carson Holt-2
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 <[hidden email]> 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
_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org