[maker-devel] keep_preds parameter

[Carson Holt]

True.  Daniel had the numbers backwards (I often accidentally do that as
well).

--Carson


On 4/7/14, 10:31 AM, "dhivya arasappan" <darasappan at gmail.com> wrote:

>Thank you Daniel. But I thought an AED score of zero indicates complete
>agreement of annotation to evidence and that 1 would mean no agreement?
>
>Dhivya
>
>On Apr 7, 2014, at 11:06 AM, Daniel Ence <dence at genetics.utah.edu> wrote:
>
>> Hi Dhivya, 
>> 
>> That's a correct understanding of keep_preds, and it is a binary
>>parameter; you either tell MAKER to keep the unsupported predictions or
>>not to keep the unsupported predictions. In the output, you can tell
>>which genes are supported by the _AED attribute in the gff3 file. Genes
>>with and AED equal to zero have no support from the evidence sets
>>(protein and EST and alt_EST).
>> 
>> ~Daniel
>> On Apr 7, 2014, at 9:57 AM, dhivya arasappan <darasappan at gmail.com>
>> wrote:
>> 
>>> Hello,
>>> 
>>> I’m looking for a little more explanation about keep_preds parameter.
>>>The documentation says that it is a threshold to add unsupported gene
>>>predictions. Along with some other changes, I set keep_preds=1 and saw
>>>a huge jump in the number of genes I was getting. Is setting this
>>>parameter to 1 equivalent to saying, include all predicted genes in my
>>>output, even if they are not supported by my set or protein data?  Is
>>>there a way to tell from my output which genes are unsupported and
>>>which are not?  Also, are the only two options for this parameter 0 and
>>>1?
>>> 
>>> Thanks
>>> dhivya
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org