make use of other gene finders in maker

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make use of other gene finders in maker

Quanwei Zhang
Hello:

I am trying to annotate the new genome of  a rodent species. I saw a clear pipeline to train the SNAP gene finder. But not clear what I should do if I also want to include augustus and/or GeneMark. Do I need to (could I and how) train it in Maker? In one of recently published paper, they mention the augustus was trained in Maker, but I am not clear how to do it? I wonder what's you opinions on using other gene finders in Maker. Thanks

"Unique features of a global human ectoparasite identified through sequencing of the bed bug genome." Nat Commun, 2016. In this paper, the training step was described as below.
Three rounds of training of the Augustus and SNAP gene predictors within Maker were used to bootstrap to a high-quality training set.


Best
Quanwei

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Re: make use of other gene finders in maker

Daniel Ence
Hi Quanwei, 

MAKER will run Augustus, SNAP, genemark or Fgenesh internally. You can also provide predictions from other gene predictors in valid GFF3 format in the “pred_gff" field in the maker_opts control file. Genemark is self training on your genome. You provide a path to the “es.mod” file that Genemark makes in the “gmhmm” field. For augustus, the training is more involved, but is described here: http://www.molecularevolution.org/molevolfiles/exercises/augustus/training.html

Augustus, snap, Fgenesh, and genemark are all complementary in some respects, but Augustus usually provides the most predictions that MAKER ends up selecting to promote to models. 

Hope that helps, 
Daniel


Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

On Feb 8, 2017, at 10:45 AM, Quanwei Zhang <[hidden email]> wrote:

Hello:

I am trying to annotate the new genome of  a rodent species. I saw a clear pipeline to train the SNAP gene finder. But not clear what I should do if I also want to include augustus and/or GeneMark. Do I need to (could I and how) train it in Maker? In one of recently published paper, they mention the augustus was trained in Maker, but I am not clear how to do it? I wonder what's you opinions on using other gene finders in Maker. Thanks

"Unique features of a global human ectoparasite identified through sequencing of the bed bug genome." Nat Commun, 2016. In this paper, the training step was described as below.
Three rounds of training of the Augustus and SNAP gene predictors within Maker were used to bootstrap to a high-quality training set.


Best
Quanwei
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
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