[maker-devel] re-annotation

[Carson Holt]

So map_forward=1, will only maintain names derived from model_gff onto new
or updated models.  Could you try either 2.28 or 2.30-beta, just to see if
this is something that is already fixed.

Thanks,
Carson


On 11/13/13 6:16 AM, "Kymberlie Hallsworth-Pepin"
<kpepin at genome.wustl.edu> wrote:

>
>We are using v2.26. We recreated the gff3 file and I can now get gene
>predictions to show up using the pred_gff file as input for the gene set.
>The naming is not maintained with the map_forward=1 as I would expect,
>just the source field in the input gff file is added to the new maker
>name.  If I change the input to a model_gff file I still do not get
>predictions in the maker gff file.
>
>thanks
>Kym
>
>
>
>
>On Tue, 12 Nov 2013, Carson Holt wrote:
>
>> They should be maintained.  What version are you using?
>>
>> --Carson
>>
>>
>> On 11/11/13 1:01 PM, "Kymberlie Hallsworth-Pepin"
>> <kpepin at genome.wustl.edu> wrote:
>>
>>> Hi Carson,
>>>
>>> I am trying to take an existing gene set and update it using new
>>> proteins.
>>> I have the gene set in gff3 format - validated as ok - and have put it
>>>in
>>> the model_gff line. I set the protein db to the new database and I set
>>> the
>>> map_forward=1 to maintain naming, but the output has no gene
>>>predictions
>>> in it. I have tried setting keep_preds both 0 and 1. I have put the gff
>>> file in both the pred_gff and model_gff and just in the pred_gff field,
>>> but I still don't get any predictions maintained. Can you tell me what
>>>I
>>> might be missing ?
>>>
>>> thanks
>>> Kym
>>>
>>>
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