Hi Yealing

This should work and I am not sure why your not seeing that. For example:

chr1    artemis gene    210     720     .       +       .       ID=x
chr1    artemis mRNA    210     720     .       +       .
chr1    artemis exon    210     280     .       +       .       Parent=x.rna
chr1    artemis exon    291     720     .       +       .       Parent=x.rna

this uses the Parent qualifier of the mRNA to join the two exons.

The mRNA's are greyed out but you can still select and edit them. There
should be an option to change this (and there is with chado database
entries) so I will include that for GFF entries. When you right click on the
feature display there will then be an option to 'Show/Hide Features...'.
This will appear in the next development release.


On 9/20/11 9:06 AM, "Yealing" <yealingt+arte...@gmail.com> wrote:

> Hi All
> I've switched over to using GFF3 some time ago simply because it's the
> preferred file format for most software. Since then, I've been having
> some problem in artemis. I've tried to dig, but maybe because I have
> not digged deep enough... Please, anyone, if you can help.
> During annotation, I write GFF3 files according to the guide on
> http://www.sequenceontology.org/gff3.shtml. However, because there
> isn't an artemis GFF validator, valid GFF3 files still have problems
> in artemis. The Parent tag is supposed to be able to group exons into
> transcripts (mRNA?) and transcripts into genes. However, the features
> with identical Parent tags are not linked in artemis. Why is this so?
> I also have problems with features I mark as mRNAs. When I load the
> GFF files in artemis, in most cases the mRNA are greyed out in the
> feature list. I rana search and found in one of the artemis paper that
> this means the feature is "hidden". But I could not find a switch to
> "unhide" it. When I generate new mRNA feature in artemis, it is not
> hidden by default. Can I change this? If not, can I at least unhide it
> individually?
> Thank you!
> Yealing.
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