Hi Ed, Thanks so much for taking the time to help me out! I performed the steps you listed, as there was a difference in what I had been doing in that previously I had been loading the sequence along with the gff3 file. Still had the same issue, so I decided to start from scratch and reinstall Apollo... and it works! maybe the issue was specific to the version I had, which was not the most current one. So now I'm happily curating and annotating :)
Cheers, Elizabeth On Tue, May 25, 2010 at 12:04 AM, Ed Lee <[email protected]> wrote: > Hi Elizabeth, > > I can't seem to replicate the issue you're having. This is the steps > I've followed: > > 1) Loaded the Genbank file > 2) Appended the GFF3 data (with "Embedded FASTA in GFF" checked, since > the genomic sequence is already loaded > 3) Dragged a transposon from the results track into the annotation > track > 4) The newly created feature showed both the sequence in "Sequence..." > and the data in the "Annotation Info Editor..." > > I've tried it in both Ubuntu and Mac OSX and they both seem to > behave correctly. > > Genbank files always tend to be a cause of trouble, so if you're > successful in loading the GBK file and appending the GFF3 data, > I would sugest to then save it to GAME XML format, with both > "Save annotations" and "Save evidence (computational results)" > checked so that you retain all the data and work with a structured > format that Apollo will handle much better. > > Cheers, > Ed > > > On Thu, 20 May 2010, elizabeth henaff wrote: > > Hi Ed, >> I've tried either dragging a result into the annotation panel, and also >> creating a new annotation, and for both whenever I launch the AIE or the >> sequence it pulls up a blank window. This is also the case for annotations >> that are part of the data that I load. >> I have a gff3 file of results, and a GenBank file of annotations. I've >> tried various combinations (like, loading the genebank then layering on >> the >> gff3, or saving the genbank as chado or game and layering that onto the >> gff3, or saving both the genbank and the gff3 together as chado or game, >> and >> loading them as one) thinking that it might be the data format, but to no >> avail. >> >> To be able to layer on results when I load the genbank data I modified >> genbank.style and set ShowResults to "true". >> I've attached the .style and .tiers files and data I'm using, thanks for >> any >> help!! >> >> cheers, >> >> elizabeth >> >> On Wed, May 19, 2010 at 10:31 PM, Ed Lee <[email protected]> wrote: >> Hi Elizabeth, >> >> Are you just dragging the features from the results panel into >> the >> annotation panel and then trying to launch the AIE? Or are >> there >> any steps in between? Perhaps you can provide me with a sample >> of your data and all the steps you're doing and I'll try to >> replicate it and help out. >> >> Cheers, >> Ed >> >> >> On Wed, 19 May 2010, elizabeth henaff wrote: >> >> Hello! >> Well, I have successfully managed to load all my >> computational results into >> Apollo (thanks Ed) and now I'd like to manually curate >> these... When I drag >> a result from the black section to the blue one it makes a >> new annotation, >> but when I right-click on this and select Sequence or >> Annotation Information >> Editor, a blank window pops up. >> I'm running version 1.11.12 on Ubuntu. >> >> Thanks for any help! >> >> Cheers, >> >> Elizabeth >> >> >> >>
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