Re: [Cg-pipeline-users] additional predictor

[Lee K. <ls...@gm...>]

This looks like something that I need to understand further.  Unfortunately
I am on furlough and so I am wrapping up everything right now.  Please keep
this project folder on-hand though because this is a very relevant analysis
that will help CG-Pipeline in the future.


On Sun, Sep 29, 2013 at 11:26 PM, kok <kok...@gm...> wrote:

>  Dear Lee Katz,
>
>   condition evidence CDS  w/o prodigal 1 6048  w prodigal 1 8263  w
> prodigal 2 6192  w prodigal 3 5683  w prodigal 4 875
> Table above shows the statistics of the results that I have got for the
> test on several evidence value. It seems that evidence 2  is the one that I
> would like to proceed for as it returns with the most CDS which by manual
> check I can see some are collected from just prodigal and BLAST evidence
> that missed from previous CGP without prodigal included.
>
> However, I find out that the coordinates of the CDS from BLAST and
> prodigal recorded with infinity "complement(1617923..inf)". From the
> run_prediction scripts I see that the prodigal is not used for reconcile
> prediction which I am not sure whether it's the cause of the error, but
> including prodigal for the start prediction during prediction
> reconciliation will be good as I have seen cases that prodigal are doing
> better with the start prediction compared to the other predictors. Hope
> this is easy to be implemented and thanks for your time.
>
> Regards,
> Kok
>
>
>
> On 12/8/2013 7:25 PM, Lee Katz wrote:
>
> I know!  Prodigal is just so easy to use, and so it was really easy to
> make a wrapper around it.
>
>  2/4 might be ok too, but I do not have enough time to perform any
> rigorous tests to see which way is better.  If you have time, please let me
> and the community know which gives you better results.  I think it would be
> informative to know what 1/4, 2/4, 3/4, and 4/4 gives you for each genome.
>  There is an interesting table that the Georgia Tech compgenomics class
> created this year, at
> http://compgenomics2013.biology.gatech.edu/index.php/Gene_Prediction_Group#Gene_Prediction_Pipeline.
>
>
>  The way to change the minimum number of predictors is to alter the
> variable $$settings{min_predictors_to_call_orf} in run_prediction.
>
>  Around line 161 in run_prediction, where it says something like
> # Categorize and reconcile predictions
> Set it back to 2 so that you can have 2/4 predictors.
>
>  $$settings{min_predictors_to_call_orf}=2;
>
>
> On Sun, Aug 11, 2013 at 11:57 PM, kok wei <kok...@gm...> wrote:
>
>> Wow, that's very great and it's faster than planned. I will certainly try
>> out the pipeline on my genome and update you with the results. I'm thinking
>> of probably having 2/4 evidence will be good enough as false positive is
>> preferred over false negative for the gene prediction, any opinion?
>>
>> Thanks for your efforts and helps.
>>
>>
>>
>> On Sun, Aug 11, 2013 at 7:35 PM, Lee Katz <ls...@gm...> wrote:
>>
>>> Hi Kok, I added a script run_prediction_prodigal.pl into source
>>> control.  It outputs a GFF file of CDS predictions.  I also made sure it
>>> outputs the training file to the temporary directory because it seems like
>>> you are interested in the training files.
>>>
>>>  I also modified run_prediction and the CGPipelineUtils module so that
>>> it predicts alongside the other predictors.  Lastly, I added an option
>>> prediction_use_prodigal = 1 under the config file so that you can enable it
>>> for run_prediction.  With Prodigal, each gene must have 2/3 or 3/4 majority
>>> to be called (depending on whether you use genemark too).
>>>
>>>  I'm new to prodigal, so please let me know if it all looks correct.
>>>  The command seems simple enough but I don't know if there are
>>> any idiosyncrasies to be aware of.
>>>
>>>
>>> On Fri, Aug 2, 2013 at 11:32 PM, Gmail <kok...@gm...> wrote:
>>>
>>>>  Thanks Jay and Lee. It will be great if the option is added. I like
>>>> prodigal for their better start prediction (from what i get for my test
>>>> genome) and less false prediction for bacterial genome as claimed. Looking
>>>> forward to the update, thanks!
>>>>
>>>>  On 02/08/2013, at 23:51, Lee Katz <ls...@gm...> wrote:
>>>>
>>>>   I'm returning to the US and back to work on Aug 12. It sounds like a
>>>> worthy addition.
>>>>
>>>>   I like prodigal but never bothered to put it in as an option. I
>>>> think it could be something optional like genemark and would be preferred
>>>> if not using genemark. In this way, CGP would still be able to have a
>>>> majority for gene calling even if you don't have genemark.
>>>>
>>>> On Aug 2, 2013, at 15:43, Jay <jhu...@gm...> wrote:
>>>>
>>>>   As far as I know, there is no convenient way of doing this. The
>>>> run_prediction script would have to be modified to support running it and
>>>> parsing the results.
>>>>
>>>> On 02/08/2013 22:52, kok wrote:
>>>>
>>>> Is it possible for cg pipeline to include the results of other *ab-initio
>>>> *predictor (eg. prodigal)? Is there any development for this function?
>>>> Or if I would like to use prodigal in place of genemark (if only two
>>>> predictors allowed), can I convert the results of prodigal into
>>>> genemark-like gm_out.lst file for cg pipeline's run_predict as a simple
>>>> modification?
>>>>
>>>> - kok -
>>>>
>>>>
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>>>
>>>
>>>   --
>>> Lee Katz, Ph.D.
>>>
>>
>>
>
>
>  --
> Lee Katz, Ph.D.
>
>
>


-- 
Lee Katz, Ph.D.