[maker-devel] loading scaffold features into chado

[Carson Holt]

>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
>
>
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