[COGE-791] SynFind feature requests Created: 21/Nov/16  Updated: 21/Nov/16

Status: Open
Project: CoGe
Component/s: SynFind
Affects Version/s: None
Fix Version/s: None

Type: Task Priority: Minor
Reporter: Matt Bomhoff Assignee: Unassigned
Resolution: Unresolved Votes: 0
Labels: None


Feature requests from M. Woodhouse on 11/14/16. See original support email for screenshots.

1. The downloadable outputs include the chromosome for each gene model, but not the start/stop. I was wondering if you could have the outputs include the start-stop too, or at least have that be an option. I understand that with multiple subject genomes it could make it a very large file, but It would be nice to have the coordinates included for each gene model for each genome so a user does not have to add them later.

2. For some genomes, such as maize v4, you have to enter the CDS name, not just the gene model name, for it to come up in the query:

Entering just the gene model name brings up nothing:

3. When Point 2 happens, the outputs for the query and/or subject are not the gene model coordinates, but the transcript or CDS coordinates, with every transcript or CDS of the gene model represented: such as the following (I had changed the headers for this file from the default):

This makes it necessary to collapse them into gene models, and makes it confusing to others when I share the link to the output for their own use. This does not happen with ALL genomes, only some of them, and it is probably related to how the gff files are annotated for each genome, so I am not sure how this could be fixed without tinkering with each gff file.

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