[maker-devel] loading scaffold features into chado

[claudia]

To whom it may concern,

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?

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?

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.

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