[maker-devel] Using GeneMark-ET with RNAseq intron hints

[Daniel Ence]

Hi Ray,

I think you’re on the right track with training Genemark with RNAseq data. It should only change the training steps, which are external to MAKER, but not how MAKER runs Genemark. You’ll still give MAKER the path to the “es.mod" file made by Genemark.

For the 2nd question, in the MAKER beta 3, MAKER creates a control file for EVM, in which you set your weights for the various inputs, and then MAKER runs EVM alongside all the other gene predictors and chooses the model that is best supported by the evidence.

~Daniel

On Feb 14, 2017, at 7:38 AM, Ray Cui <rcui at age.mpg.de<mailto:rcui at age.mpg.de>> wrote:

Hello,

         I have sucessfully installed Maker beta 3, working with both Augustus and SNAP. I also want to try adding GeneMark-ES to the ab initio predictor.
         When I read the GeneMark-ES manual, it says that one can use RNAseq data to aid training. I'm wondering what would be the best way to integrate Genemark-ET predictions into Maker. Should I run Genemark-ET independent of Maker, then integrate the GFF at some point during the maker process? If so, how should I edit the configuration file? Currently maker has an option called "gmhmm". Should I then train GeneMark by myself with RNAseq data, then feed the hmm to maker?

          And perhaps an unrelated question is that now Maker beta 3 supports EVM. I'm wondering how EVM is used by Maker (at which step, what does it do), and how does it differ from what Maker is designed for (both reconciles different gene models).

Best Regards,
Ray

Dr. Rongfeng (Ray) Cui
Max-Planck-Institut für Biologie des Alterns / Max Planck Institute for Biology of Ageing
Wissenschaftlicher MA / Postdoctoral researcher
Office: Joseph-Stelzmann 9b, D-50931 Köln / Cologne
Postal address: Postfach 41 06 23, D-50866 Köln / Cologne
Tel.:+49 (0)221 496
Mobile:           +49 0221 37970 496
rcui at age.mpg.de<mailto:rcui at age.mpg.de>
www.age.mpg.de<http://www.age.mpg.de/>


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