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

[Carson Holt]

The names of scripts used are listed in the maker_exe.ctl file. It depends on if formatting or any flags have changed between versions.

—Carson


> On Feb 20, 2017, at 1:59 AM, Ray Cui <rcui at age.mpg.de> wrote:
> 
> 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 <mailto:rcui at age.mpg.de>
> www.age.mpg.de <http://www.age.mpg.de/> 
> 
> 
> 
> On Mon, Feb 20, 2017 at 6:39 AM, Carson Holt <carsonhh at gmail.com <mailto: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 <mailto: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 <tel:+49%20221%20496> 
>> 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/> 
>> 
>> 
>> 
>> On Tue, Feb 14, 2017 at 3:43 PM, Ence,daniel <d.ence at ufl.edu <mailto: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 <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 <tel:+49%20221%20496> 
>>> 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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>> 
>> 
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