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

[Ray Cui]

Dear Carson,

        I have now run GeneMark-ET, and it produces a trained .mod file. I
think it can be then passed to Maker. Do you know what is the final
constructed command line in Maker that calls genemark? Genemark-et and es
use the same perl script so one probably only needs to use the
 --prediction  and --predict_with xxx.mod options to predict genes using
the species specific parameters (bypassing regular training and prediction
steps)


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



On Mon, Feb 20, 2017 at 6:39 AM, Carson Holt <carsonhh at gmail.com> wrote:

> MAKER was support was designed with GeneMark-ES. It may or may not work
> with GeneMark-ET. So any MAKER related archive posts etc. will be related
> to the latter.
>
> With GeneMark-ES, you simply provided a genome assembly and let it run. It
> would then produce several files and output directories. The es.mod file
> was the one you provided to MAKER. I don’t know how this compares
> to GeneMark-ET.
>
> —Carson
>
>
>
> On Feb 14, 2017, at 8:44 AM, Ray Cui <rcui at age.mpg.de> wrote:
>
> 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 <+49%20221%20496>
> 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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