[maker-devel] loading scaffold features into chado

[Carson Holt]

Yes. thank you Scott.  My answer would work for GBrowse NOT Chado :-)

--Carson



On 12-03-20 1:25 PM, "Scott Cain" <scott at scottcain.net> wrote:

>Hi Claudia,
>
>I agree with everything that Carson wrote, except about name
>searching--it's a little trickier in Chado.  What you probably want to
>do is implement full text searching.  See:
>
>  http://gmod.org/wiki/Chado_Full_Text_Search
>
>for more information on setting it up and maintaining it.
>
>Scott
>
>
>On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt <carsonhh at gmail.com> wrote:
>>
>>>I have 2 concerns, the first is:  regarding representing scaffold
>>>features in chado and gbrowse. I noticed that the Sequence ontology uses
>>>the term supercontig and so if my assembly generated scaffolds entitled
>>>"scaffold" should I change the names to supercontigs so that chado
>>>recognizes the terms?
>>
>> Yes.  You must use valid SO terms.  It is a requirement of GFF3, and
>>Chado
>> will enforce this requirement on loading a GFF3 file (note Chado will
>>even
>> go as far as to check the validity of the Ontology_term= attribute in
>>GFF3
>> if you use it).  You can decide to use contig or supercontig as your
>> sequence feature.  It doesn¹t really matter unless you are placing both
>> into the database as separate features (i.e. You have a supercontig as
>>the
>> parent feature and then you enter contigs individually as children of
>>the
>> supercontig).
>>
>>
>>>
>>>Corresponding to my first question, Maker does not know that the contigs
>>>are actually scaffold/supercontigs when annotating and so Maker will
>>>still call the "type" feature or column 3 in the GFF3, a 'contig', how
>>>can Maker be implemented to change this naming convention before
>>>annotation, or after?
>>
>> Not really important unless you plan on making contigs children of the
>> supercontig.  But you can always do a search and replace. -->
>> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print $_' >
>> new_file.gff
>>
>>
>>>
>>>Consequently, I am having problems pulling up gene features in Gbrowse
>>>when doing a generic gene search, and I must provide the maker generated
>>>unique-gene_id in the gbrowse search bar or the known sequence id i.e
>>>'scaffold001', which is not useful for someone who does not have this
>>>information.
>>>---- I do not have this problem when my seq_id, and 'type' feature id
>>>match in the true case of 'contigs'. I can do a generic gene search in
>>>gbrowse with the term 'maker' and gbrowse will provide me all the
>>>associated maker generated gene calls.
>>
>> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
>> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>>
>>
>> Thanks,
>> Carson
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>>
>>>Thank you for any guidance resolving these concerns,
>>>Claudia
>>>
>>>
>>>
>>>--
>>>Claudia DiNatale
>>>Master's Candidate
>>>The Crosby Lab
>>>University of Windsor
>>>519-253-3000 ext: 4755
>>>
>>>
>>>_______________________________________________
>>>maker-devel mailing list
>>>maker-devel at box290.bluehost.com
>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>>
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>
>
>
>-- 
>------------------------------------------------------------------------
>Scott Cain, Ph. D.                                   scott at scottcain
>dot net
>GMOD Coordinator (http://gmod.org/)                     216-392-3087
>Ontario Institute for Cancer Research