[maker-devel] est2genome option

[Felix Bemm]

dear all,

I am using a transcriptome and a cegma annotation to run the first maker
iteration. Based on the resulting genes I build a snap model and start
the second iteration. The transcriptome and the cegma annotation are
passed through. What is the option est2genome (set to 1) doing in this
case? Is it somehow preferred over any other prediction method? Is it
useful to switch on several predictors during one run? And my last
question, if the switch for repeat masking pass through is on does this
mean that maker is not running any rm computations?

best regards
felix

--
Felix Bemm
Department of Bioinformatics
University of Würzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix...@uni-wuerzburg.de

_______________________________________________
maker-devel mailing list
maker...@box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

[Carson Holt]

est2genome is primarily used when you don’t have any trained predictors.  It will produce models directly from the ESTs (these will almost always be partial).  These models can then be used to train predictors like SNAP.  If you’ve used CEGMA to train SNAP, you won’t necessarily get any benefit from running est2genome (it is really just to give you a starting point).  To improve SNAP after any initial training, you can run MAKER with just SNAP (no est2genome) and the with all evidence (proteins and ESTs) and then retrain on the evidence informed annotations.  A single round of this is sufficient.

The -R flag on the command line will turn off all repeat masking (this will override any values you may have filled in the control files).  You can also just turn on and off individual options in the control files (a blank option means it is off).  Anything with a value will run, i.e. If model_org=fly is set then RepeatMasker will run on the fly subset of RepBase.

Thanks,
Carson

Carson Holt
Graduate Student
Yandell Lab
http:/www.yandell-lab.org/
Eccles Institute of Human Genetics
University of Utah