[maker-devel] errors in final gff

[Carson Holt]

Also note that ID= must be unique. Name= does not have to be, and won't be
if the same protein or repeat element aligns to more than one location for
example.

Thanks,
Carson


On 6/20/14, 3:50 PM, "Carson Holt" <carsonhh at gmail.com> wrote:

>did you use est_forward?  Also in the example you showed all the IDs are
>unique (one says hit and the other hsp in the ID, so they are different)?
>Could you find the non-uunique IDs causing the error?
>
>--Carson
>
>
>On 6/19/14, 2:05 AM, "Anurag Priyam" <anurag08priyam at gmail.com> wrote:
>
>>I used est_gff= option, which refers to a GFF file generated by
>>cufflinks2gff3. The erroneous annotations didn't come from this GFF.
>>
>>-- Priyam
>>
>>On Thu, Jun 19, 2014 at 3:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>> Are you passing in old data via GFF3?
>>>
>>> --Carson
>>>
>>>
>>> On 6/18/14, 12:15 PM, "Anurag Priyam" <anurag08priyam at gmail.com> wrote:
>>>
>>>>It's version 2.31.
>>>>
>>>>-- Priyam
>>>>
>>>>On Wed, Jun 18, 2014 at 11:41 PM, Carson Holt <carsonhh at gmail.com>
>>>>wrote:
>>>>> What MAKER version are you using?
>>>>>
>>>>> --Carson
>>>>>
>>>>>
>>>>> On 6/18/14, 11:44 AM, "Anurag Priyam" <a.priyam at qmul.ac.uk> wrote:
>>>>>
>>>>>>Hi,
>>>>>>
>>>>>>I compiled all annotations generated by MAKER into a single GFF file
>>>>>>using the gff3_merge script distributed with MAKER. While formatting
>>>>>>this GFF for use with JBrowse, I found a few errors:
>>>>>>
>>>>>>1. Three instances where two features were assigned the same id.
>>>>>>2. One instance where a group of three subfeatures refer to a
>>>>>>non-existent parent.
>>>>>>
>>>>>>Here is the relevant portion of the GFF file:
>>>>>>https://gist.github.com/yeban/ffaf5cd419639dd073a7
>>>>>>
>>>>>>I worked around the issue temporarily for the job at hand, but I am
>>>>>>left wondering why would these errors creep in.
>>>>>>
>>>>>>-- Priyam
>>>>>>
>>>>>>_______________________________________________
>>>>>>maker-devel mailing list
>>>>>>maker-devel at box290.bluehost.com
>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o
>>>>>>r
>>>>>>g
>>>>>
>>>>>
>>>
>>>
>
>