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

[Ray Cui]

Hi Daniel,

        thanks! It seems that Genemark-ET has a "--training" flag, is that
the flag I should use when training or should I just let Genemark also
perform the prediction?

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



On Tue, Feb 14, 2017 at 3:43 PM, Ence,daniel <d.ence at ufl.edu> wrote:

> 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> 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 <+49%20221%20496>
> Mobile:           +49 0221 37970 496
> rcui at age.mpg.de
> www.age.mpg.de
>
>
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>
>
>
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