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

[Ray Cui]

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
www.age.mpg.de
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