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 . + . ID=x.rna;Parent=x 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. Regards Tim 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. > > _______________________________________________ > Artemis-users mailing list > Artemis-users@sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
