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GMOD / Apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.
http://genomearchitect.readthedocs.io/
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allow for export of FASTA re-assembled #2349

Open nathandunn opened 4 years ago

nathandunn commented 4 years ago

From this:

https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/vTNqtZSfl5M

The basic idea would be to allow an export option where the output FASTA would be re-assembled within Apollo, instead of just an annotation with the original in place.

nathandunn commented 4 years ago

Would have multiple places to allow fixes:

1 - have a checkbox that is "integrate assembly correction"

image

2 - and have a checkbox here as well:

image

It could be done on the track as well, but would rather not add to the dojo interface.

3 - extend the option to other types (GFF3, VCF) to automatically calculate in the downstream coordinates

abretaud commented 4 years ago

It would be great also if there was a way to have the same kind of option when exporting GFF: if there are some insertions/deletions the downstream features coordinates needs to be modified too. Currently it can be done after export with some script looking at the GFF and the VCF, but it's not ideal

nathandunn commented 4 years ago

I see. The model is modified become of the correction, but the actual coordinates are not. I agree. Makes sense. I updated this ticket for that.